Available Modules
Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.
ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).
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ancestry_fractions allele_frequencies versions
Read CEL files into an ExpressionSet and generate a matrix
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rds expression annotation versions
Methods for Affymetrix Oligonucleotide Arrays
Annotation and Ranking of Structural Variation
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tsv unannotated_tsv vcf versions
Annotation and Ranking of Structural Variation
Install the AnnotSV annotations
NO input
annotations versions
Annotation and Ranking of Structural Variation
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
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translated_mrna total_mrna translation buffering mrna_abundance rdata fold_change_plot interaction_p_distribution_plot residual_distribution_summary_plot residual_vs_fitted_plot rvm_fit_for_all_contrasts_group_plot rvm_fit_for_interactions_plot rvm_fit_for_omnibus_group_plot simulated_vs_obt_dfbetas_without_interaction_plot session_info versions
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
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tif versions
Use deamination patterns to estimate contamination in single-stranded libraries
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txt versions
Estimates present-day DNA contamination in ancient DNA single-stranded libraries.
BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.
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fastq log versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
Converts certain output formats to VCF
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vcf_gz vcf bcf_gz bcf hap legend samples tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Index VCF tools
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csi tbi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.
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vcf tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available
Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
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vcf tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
Merges methylation information for opposite-strand C's in a CpG context
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bed versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Construct species phylogenies using BUSCO proteins
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gene_trees supermatrix versions
Construct species phylogenies using BUSCO proteins
Construct the database necessary for checkv's quality assessment
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checkv_db versions
Assess the quality of metagenome-assembled viral genomes.
Construct the database necessary for checkv's quality assessment
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checkv_db versions
Assess the quality of metagenome-assembled viral genomes.
Determine the allelic profiles of a genome using a pre-defined schema
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stats contigs_info alleles log paralogous_counts paralogous_loci cds_coordinates invalid_cds loci_summary_stats versions
A complete suite for gene-by-gene schema creation and strain identification.
Create a schema to determine the allelic profiles of a genome
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schema cds_coordinates invalid_cds versions
A complete suite for gene-by-gene schema creation and strain identification.
Builds a classic bloom filter COBS index
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index versions
Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
Builds a compact bloom filter COBS index
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index versions
Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
Dump a coolerโs data to a text stream.
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bedpe versions
Sparse binary format for genomic interaction matrices
structural-variant calling with cutesv
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vcf versions
Call structural variants
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bcf csi versions
Structural variant discovery by integrated paired-end and split-read analysis
runs a differential expression analysis with DESeq2
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results dispersion_plot rdata size_factors normalised_counts rlog_counts vst_counts model session_info versions
Differential gene expression analysis based on the negative binomial distribution
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
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vcf versions
Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.
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vcf tbi versions
Provide the SNP coverage of each individual in an eigenstrat formatted dataset.
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tsv json versions
A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.
EMM typing of Streptococcus pyogenes assemblies
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tsv versions
Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through task.ext.args.
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cache versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.
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output versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through task.ext.args.
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vcf tbi tab json report versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Searches a term in a public NCBI database
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xml versions
Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Queries an NCBI database using Unique Identifier(s)
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xml versions
Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Queries an NCBI database using an UID
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txt versions
Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
estimation of the unfolded site frequency spectrum
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sfs_out pvalues_out versions
Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly
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dropset okayset versions
EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.
Estimate repeat sizes using NGS data
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vcf json bam versions
Merge STR profiles into a multi-sample STR profile
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merged_profiles versions
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
Compute genome-wide STR profile
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locus_tsv motif_tsv str_profile versions
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
A program that counts sequence occurrences in FASTQ files.
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count_matrix stats distribution_plot reads_plot reads_plot_percentage versions
2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.
Distance-based phylogeny with FastME
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nwk stats matrix bootstrap versions
Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.
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bam versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Efficient compression tool for protein structures
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fcz versions
Foldcomp: a library and format for compressing and indexing large protein structure sets
Decompression tool for foldcomp compressed structures
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pdb versions
Foldcomp: a library and format for compressing and indexing large protein structure sets
Creates a database for Foldmason.
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db versions
Multiple Protein Structure Alignment at Scale with FoldMason
Aligns protein structures using foldmason
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msa_3di msa_aa versions
Multiple Protein Structure Alignment at Scale with FoldMason
Renders a visualization report using foldmason
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html versions
Multiple Protein Structure Alignment at Scale with FoldMason
Create a database from protein structures
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db versions
Foldseek: fast and accurate protein structure search
Search for protein structural hits against a foldseek database of protein structures
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aln versions
Foldseek: fast and accurate protein structure search
Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.
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lineages summarized versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
Performs local realignment around indels to correct for mapping errors
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bam versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Generates a list of locations that should be considered for local realignment prior genotyping.
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intervals versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
SNP and Indel variant caller on a per-locus basis
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vcf versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
estimates the parameters for the DRAGstr model
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dragstr_model versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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split_read_evidence split_read_evidence_index paired_end_evidence paired_end_evidence_index site_depths site_depths_index versions
Genome Analysis Toolkit (GATK4)
This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
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str_table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Create a panel of normals constraining germline and artifactual sites for use with mutect2.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
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printed_evidence printed_evidence_index versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Splits CRAM files efficiently by taking advantage of their container based structure
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split_crams versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Splits reads that contain Ns in their cigar string
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.
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annotated_vcf index versions
Genome Analysis Toolkit (GATK4)
Clusters structural variants based on coordinates, event type, and supporting algorithms
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clustered_vcf clustered_vcf_index versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.
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output ped bed bed_index roc html png versions
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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bedpe bed versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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vcf versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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bedpe bed versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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high_conf_sv all_sv versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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high_conf_sv all_sv versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Collapse redundant transcript models in Iso-Seq data.
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bed bed_trans_reads local_density_error polya read strand_check trans_report versions varcov variants
Collapse similar gene model
GenomeTools gt-gff3validator utility to strictly validate a GFF3 file
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success_log error_log versions
The GenomeTools genome analysis system
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
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fasta gff vcf stats phylip embl_predicted embl_branch tree tree_labelled versions
Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
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gbk svg tsv versions
Pre-compute the graph index structure.
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graph versions
HLA typing from short and long reads
Create a tag directory with the HOMER suite
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tagdir taginfo versions
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Differential gene expression analysis based on the negative binomial distribution
Empirical Analysis of Digital Gene Expression Data in R
Search covariance models against a sequence database
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output alignments target_summary versions
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification
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profile snvs gene_info genome_info linkage mapping_info scaffold_info versions
Calculation of strain-level metrics
Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments.
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phylogeny report mldist lmap_svg lmap_eps lmap_quartetlh sitefreq_out bootstrap state contree nex splits suptree alninfo partlh siteprob sitelh treels rate mlrate exch_matrix log versions
Construct KMCP database from k-mer files
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kmcp log versions
Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Bayesian reconstruction of ancient DNA fragments
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bam fq_pass fq_fail unmerged_r1_fq_pass unmerged_r1_fq_fail unmerged_r2_fq_pass unmerged_r2_fq_fail log versions
Lofreq subcommand to remove variants with low coverage or strand bias potential
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vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.
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vcf tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi somatic_sv_vcf somatic_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi tumor_sv_vcf tumor_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
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runtime_log fragmisincorporation_plot length_plot misincorporation lgdistribution dnacomp stats_out_mcmc_hist stats_out_mcmc_iter stats_out_mcmc_trace stats_out_mcmc_iter_summ_stat stats_out_mcmc_post_pred stats_out_mcmc_correct_prob dnacomp_genome rescaled pctot_freq pgtoa_freq fasta folder versions
Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
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maxquant_txt versions
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input.
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tif versions
Staging modules for MCMICRO
Strain-level metagenomic assignment
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wimp evidence_unknown_species reads2taxon em contig_coverage length_and_id krona versions
A tool to estimate bacterial species abundance
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results versions
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.
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outputs versions
miRDeep2 Mapper (mapper.pl) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.
A tool to reconstruct plasmids in bacterial assemblies
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chromosome contig_report plasmids mobtyper_results versions
Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
msisensor2 detection of MSI regions.
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msi distribution somatic versions
MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.
Aligns protein structures using mTM-align
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alignment structure versions
Algorithm for structural multiple sequence alignments
Parallel implementation of the gzip algorithm.
SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA
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full_alignment info_txt snp_alignment snp_genome_alignment snpstatistics snptable snptable_snpeff snptable_uncertainty structure_genotypes structure_genotypes_nomissing json versions
NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
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normalized_counts normalized_counts_wo_HK versions
R package that uses two main functions to summarize and visualize NanoString RCC files,
namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates
sample specific size factors and normalises the data.
For more information vignette("NACHO") and vignette("NACHO-analysis")
NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
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nacho_qc_reports nacho_qc_png nacho_qc_txt versions
R package that uses two main functions to summarize and visualize NanoString RCC files,
namely: load_rcc() and visualise(). It also includes a function normalise(), which (re)calculates
sample specific size factors and normalises the data.
For more information vignette("NACHO") and vignette("NACHO-analysis")
Parse all the supporting reads of putative somatic SVs using nanomonsv. After successful completion, you will find supporting reads stratified by deletions, insertions, and rearrangements. A precursor to "nanomonsv get"
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insertions insertions_index deletions deletions_index rearrangements rearrangements_index bp_info bp_info_index versions
nanomonsv is a software for detecting somatic structural variations from paired (tumor and matched control) cancer genome sequence data.
Construct a dynamic succinct variation graph in ODGI format from a GFAv1.
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og versions
An optimized dynamic genome/graph implementation
Calculates a distribution of the mass error from given mass spectra and IDs.
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frag_err prec_err versions
OpenMS is an open-source software C++ library for LC-MS data management and analyses
Assign restriction fragments to pairs
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restrict versions
CLI tools to process mapped Hi-C data
Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file
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tsv versions
panacus is a tool for computing counting statistics for GFA files
Determines the depth in a BAM/CRAM file
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depth binned_depth versions
Graph realignment tools for structural variants
Genotype structural variants using paragraph and grmpy
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vcf json versions
Graph realignment tools for structural variants
Convert a VCF file to a JSON graph
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graph versions
Graph realignment tools for structural variants
pbsv - PacBio structural variant (SV) signature discovery tool
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svsig versions
pbsv - PacBio structural variant (SV) calling and analysis tools
phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
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results versions
Collect metrics about the insert size distribution of a paired-end library.
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metrics histogram versions
Java tools for working with NGS data in the BAM format
Automatically improve draft assemblies and find variation among strains, including large event detection
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improved_assembly vcf change_record tracks_bed tracks_wig versions
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data
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bp cem del dd int_final inv li rp si td versions
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data
Main caller script for peak calling
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divergent_TREs bidirectional_TREs unidirectional_TREs peakcalling_log versions
Peak Identifier for Nascent Transcripts Starts (PINTS)
Recodes plink bfiles into a new text fileset applying different modifiers
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ped map txt raw traw beagledat chrdat chrmap geno pheno pos phase info lgen list gen gengz sample rlist strctin tped tfam vcf vcfgz versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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xml txt versions
Run all Portcullis steps in one go
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log pass_junctions_bed pass_junctions_tab intron_gff exon_gff spliced_bam spliced_bai versions
Portcullis is a tool that filters out invalid splice junctions from RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes splice junctions and removes likely false positives, outputting filtered results in multiple formats for downstream analysis.
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
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phylogeny phylogeny_bootstrapped versions
Quality control of riboseq bam data
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distribution pdf offset versions
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
Infer strandedness from sequencing reads
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txt versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Calculate how mapped reads are distributed over genomic features
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txt versions
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
Uses the RTN R package for transcriptional regulatory network inference (TNI).
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tni tni_perm tni_bootstrap tni_filtered versions
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
Use seqkit to find/replace strings within sequences and sequence headers
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fastx versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
PileupCaller is a tool to create genotype calls from bam files using read-sampling methods
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eigenstrat plink freqsum versions
Tools for population genetics on sequencing data
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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tsv txt versions
SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
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log read_qual breakpoints_double read_alignments read_ids collapsed_dup loh all_vcf all_breakpoints_clusters_list all_breakpoints_clusters all_plots somatic_vcf somatic_breakpoints_clusters_list somatic_breakpoints_clusters somatic_plots versions
Serovar prediction of salmonella assemblies
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tsv allele_fasta allele_json cgmlst_csv versions
smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.
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vcf versions
structural variant calling and genotyping with existing tools, but, smoothly
structural-variant calling with sniffles
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vcf tbi snf versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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tsv html versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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extract versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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html pairs_tsv samples_tsv versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Serotype prediction of Streptococcus suis assemblies
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tsv versions
Advanced sequence file format conversions
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cram gzi versions
Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.
Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
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vcf versions
Tandem repeat genotyper for long reads
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vcf tbi versions
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
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vcf vcf_tbi genome_vcf genome_vcf_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
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vcf_indels vcf_indels_tbi vcf_snvs vcf_snvs_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Merges the annotation gtf file and the stringtie output gtf files
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gtf versions
Transcript assembly and quantification for RNA-Seq
Transcript assembly and quantification for RNA-Se
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transcript_gtf abundance coverage_gtf ballgown versions
Transcript assembly and quantification for RNA-Seq
Converts a bedpe file to a VCF file (beta version)
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vcf versions
Toolset for SV simulation, comparison and filtering
Filter a vcf file based on size and/or regions to ignore
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vcf versions
Toolset for SV simulation, comparison and filtering
Compare or merge VCF files to generate a consensus or multi sample VCF files.
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vcf versions
Toolset for SV simulation, comparison and filtering
Simulate an SV VCF file based on a reference genome
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parameters vcf bed fasta insertions versions
Toolset for SV simulation, comparison and filtering
Report multiple stats over a VCF file
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stats versions
Toolset for SV simulation, comparison and filtering
SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements
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sv indel germ_indel germ_sv som_indel som_sv unfiltered_sv unfiltered_indel unfiltered_germ_indel unfiltered_germ_sv unfiltered_som_indel unfiltered_som_sv raw_calls discordants log versions
SVbenchmark compares a set of โtestโ structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.
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fns fps distances log report versions
SVanalyzer: tools for the analysis of structural variation in genomes
Build a structural variant database
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db versions
structural variant database software
The merge module merges structural variants within one or more vcf files.
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vcf tbi csi versions
structural variant database software
Query a structural variant database, using a vcf file as query
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vcf versions
structural variant database software
Performs tests on BAF files
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metrics versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Count the instances of each SVTYPE observed in each sample in a VCF.
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counts versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert an RdTest-formatted bed to the standard VCF format.
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vcf tbi versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert SV calls to a standardized format.
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vcf versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Converts VCFs containing structural variants to BED format
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bed versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert a VCF file to a BEDPE file.
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bedpe versions
Tools for processing and analyzing structural variants
SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data
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json gt_vcf bam versions
Compute genotype of structural variants based on breakpoint depth
SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample
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gt_vcf json versions
Bayesian genotyper for structural variants
A tool to standardize VCF files from structural variant callers
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vcf tbi versions
Aligns sequences using T_COFFEE
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alignment lib versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Computes a consensus alignment using T_COFFEE
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alignment eval versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Reformats the header of PDB files with t-coffee
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formatted_pdb versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Computes the irmsd score for a given alignment and the structures.
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irmsd versions
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
Parallel implementation of the gzip algorithm.
Aligns sequences using the regressive algorithm as implemented in the T_COFFEE package
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alignment versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Parallel implementation of the gzip algorithm.
Reformats files with t-coffee
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formatted_file versions
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
Computes the coverage of different regions from the bam file.
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cov wig versions
TIDDIT - structural variant calling.
Identify chromosomal rearrangements.
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vcf ploidy versions
Search for structural variants.
Searches a genome for a telomere string such as TTAGGG
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tsv bedgraph versions
tidk is a toolkit to identify and visualise telomeric repeats in genomes
TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file.
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pep gff3 cds dat folder versions
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf
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pep gff3 cds bed versions
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
Tandem repeat genotyping from PacBio HiFi data
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vcf bam versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Merge TRGT VCFs from multiple samples
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vcf versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Given baseline and comparison sets of variants, calculate the recall/precision/f-measure
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fn_vcf fn_tbi fp_vcf fp_tbi tp_base_vcf tp_base_tbi tp_comp_vcf tp_comp_tbi summary versions
Structural variant comparison tool for VCFs
Over multiple vcfs, calculate their intersection/consistency.
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consistency versions
Structural variant comparison tool for VCFs
Normalization of SVs into disjointed genomic regions
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vcf versions
Structural variant comparison tool for VCFs
Subsample a long-read sequencing fastq file for multiple assemblies
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subreads versions
Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes
In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.
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alignment_properties_json versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Convert VCF with structural variations to CytoSure format
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cgh versions
Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.
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vcf versions
Command-line tools for manipulating VCF files
Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
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log selfsm depthsm selfrg depthrg bestsm bestrg versions
verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.
Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.
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log ud bed mu self_sm ancestry versions
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Constructs a graph from a reference and variant calls or a multiple sequence alignment file
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graph versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
Deconstruct snarls present in a variation graph in GFA format to variants in VCF format
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vcf versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
write your description here
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xg vg_index versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
calculate secondary structures of two RNAs with dimerization
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rnacofold_csv rnacofold_ps versions
calculate secondary structures of two RNAs with dimerization
The program works much like RNAfold, but allows one to specify two RNA sequences which are then allowed to form a dimer structure. RNA sequences are read from stdin in the usual format, i.e. each line of input corresponds to one sequence, except for lines starting with > which contain the name of the next sequence. To compute the hybrid structure of two molecules, the two sequences must be concatenated using the & character as separator. RNAcofold can compute minimum free energy (mfe) structures, as well as partition function (pf) and base pairing probability matrix (using the -p switch) Since dimer formation is concentration dependent, RNAcofold can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers. Output consists of the mfe structure in bracket notation as well as PostScript structure plots and โdot plotโ files containing the pair probabilities, see the RNAfold man page for details. In the dot plots a cross marks the chain break between the two concatenated sequences. The program will continue to read new sequences until a line consisting of the single character @ or an end of file condition is encountered.
Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs.
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rnafold_txt rnafold_ps versions
Calculate minimum free energy secondary structures and partition function of RNAs
The program reads RNA sequences, calculates their minimum free energy (mfe) structure and prints the mfe structure in bracket notation and its free energy. If not specified differently using commandline arguments, input is accepted from stdin or read from an input file, and output printed to stdout. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.
calculate locally stable secondary structures of RNAs
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rnalfold_txt versions
calculate locally stable secondary structures of RNAs
Compute locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+LL) memory and O(nL*L) CPU time. Thus it is practical to โscanโ very large genomes for short RNA structures. Output consists of a list of secondary structure components of size <= L, one entry per line. Each output line contains the predicted local structure its energy in kcal/mol and the starting position of the local structure.
Extracting sequences that were unbinnned by vRhyme into a FASTA file
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unbinned_sequences versions
vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
Linking bins output by vRhyme to create one sequences per bin
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linked_bins versions
vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
Binning virus genomes from metagenomes
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bins membership summary versions
vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.
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aln biom mothur otu bam out blast uc centroids clusters profile msa versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same).
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fasta clustering log versions
A versatile open source tool for metagenomics (USEARCH alternative)
Performs quality filtering and / or conversion of a FASTQ file to FASTA format.
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fasta log versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Taxonomic classification using the sintax algorithm.
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tsv versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength).
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fasta versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
Compare target sequences to fasta-formatted query sequences using global pairwise alignment.
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aln biom lca mothur otu sam tsv txt uc versions
VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)
The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.
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vcf tbi graph versions
A large variant benchmarking tool analogous to hap.py for small variants.
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report bench_vcf bench_vcf_tbi versions
The xeniumranger import-segmentation module allows you to specify 2D nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation results can be generated by community-developed tools or prior Xenium segmentation result.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.
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outs versions
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
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