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.
Screen assemblies for antimicrobial resistance against multiple databases
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report versions
Mass screening of contigs for antibiotic resistance genes
Screen assemblies for antimicrobial resistance against multiple databases
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report versions
Mass screening of contigs for antibiotic resistance genes
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
The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.
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passed_gff failed_gff versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.
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sample_dir contig_gbks db_tsv tsv faa sample_log full_log db db_txt db_fasta db_mmseqs versions
A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.
A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.
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txt versions
ANGSD: Analysis of next generation Sequencing Data
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
Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).
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tsv 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.
Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
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primary_filtered_bam contamination_bam versions
Profiles the nucleotide content of intervals in a fasta file.
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bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
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
Perform basic quality control on a BAM file generated with Biscuit
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reports versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Relates methylation calls back to genomic cytosine contexts.
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coverage report summary versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Benchmarking Universal Single Copy Orthologs
metafastamodelineagebusco_lineages_pathconfig_file
meta batch_summary short_summaries_txt short_summaries_json busco_dir full_table missing_busco_list single_copy_proteins seq_dir translated_proteins versions
Benchmarking Universal Single Copy Orthologs
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batch_summary short_summaries_txt short_summaries_json log full_table missing_busco_list single_copy_proteins seq_dir translated_dir busco_dir downloaded_lineages single_copy_faa single_copy_fna versions
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
Download database for BUSCO
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download_dir versions
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
BUSCO plot generation tool
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png versions
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).
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txt versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).
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orf2lca bin2classification log diamond faa gff versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
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orf2lca contig2classification log diamond faa gff versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Downloads the required files for either Nr or GTDB for building into a CAT database
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rawdb versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).
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rat_log complete_abundance contig_abundance read2classification alignment_diamond contig2classification cat_log orf2lca faa gff unmapped_diamond unmapped_fasta unmapped2classification versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Summarises results from CAT/BAT/RAT classification steps
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txt versions
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
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checkm_output marker_file checkm_tsv versions
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
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output fasta versions
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
CheckM2 database download
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database versions
CheckM2 - Rapid assessment of genome bin quality using machine learning
CheckM2 bin quality prediction
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checkm2_output checkm2_tsv versions
CheckM2 - Rapid assessment of genome bin quality using machine learning
Construct the database necessary for checkv's quality assessment
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checkv_db versions
Assess the quality of metagenome-assembled viral genomes.
Assess the quality of metagenome-assembled viral genomes.
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quality_summary completeness contamination complete_genomes proviruses viruses 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.
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
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self_circular extended_circular extended_partial extended_failed orphan_end all_cobra_assemblies joining_summary log versions
Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples
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args_txt clustering_csv log_txt original_data_csv pca_components_csv pca_transformed_csv versions
Clustering cONtigs with COverage and ComposiTion
Generate the input coverage table for CONCOCT using a BEDFile
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tsv versions
Clustering cONtigs with COverage and ComposiTion
Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC
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p_value_txt versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Copy number and genotype annotation from whole genome and whole exome sequencing data
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bedgraph control_cpn sample_cpn gcprofile_cpn BAF CNV info ratio config versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Plot Freec output
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bed versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Format Freec output to circos input format
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circos versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Plot Freec output
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png_baf png_ratio_log2 png_ratio versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Plot Freec output
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png_baf png_ratio_log2 png_ratio versions
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Map reads to contigs and estimate coverage
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coverage versions
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
DAS Tool binning step.
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log summary contig2bin eval bins pdfs fasta_proteins candidates_faa fasta_archaea_scg fasta_bacteria_scg b6 seqlength versions
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
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fastatocontig2bin versions
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
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scaffolds2bin versions
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
decoupler is a package containing different statistical methods to extract biological activities from omics data within a unified framework. It allows to flexibly test any enrichment method with any prior knowledge resource and incorporates methods that take into account the sign and weight. It can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.
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dc_estimate dc_pvals versions
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
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daa daa_tsv arg potential_arg versions
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
Assemble bacterial isolate genomes from Nanopore reads
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contigs log raw_contigs gfa txt versions
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
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.
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.
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.
Run falco on sequenced reads
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html txt versions
falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
Perform adapter and quality trimming on sequencing reads with reporting
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reads stats debug statspdf reads_fail reads_unpaired log versions
tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
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log txt hmm hmm_genes orfs orfs_amino contigs contigs_pept filtered filtered_pept fragments trimmed spades metagenome tmp versions
Perform adapter/quality trimming on sequencing reads
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reads json html log reads_fail reads_merged versions
fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data.
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tsv versions
Run NCBI's FCS adaptor on assembled genomes
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cleaned_assembly adaptor_report log pipeline_args skipped_trims versions
The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly.
Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.
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fcs_gx_report taxonomy_report versions
"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."
Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to remove foreign contamination from genome assemblies
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cleaned contaminants versions
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
Fetches the NCBI FCS-GX database using a provided manifest URL
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database versions
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies
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fcsgx_report taxonomy_report log hits versions
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
Filtlong filters long reads based on quality measures or short read data.
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reads log versions
fq generate is a FASTQ file pair generator. It creates two reads, formatting names as described by Illumina. While generate creates "valid" FASTQ reads, the content of the files are completely random. The sequences do not align to any genome. This requires a seed (--seed) to be supplied in ext.args.
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fastq versions
fq is a library to generate and validate FASTQ file pairs.
Annotates intervals with GC content, mappability, and segmental-duplication content
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annotated_intervals 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.
Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
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contamination segmentation 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.
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)
Determines the baseline contig ploidy for germline samples given counts data
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calls model 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.
Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
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vcf tbi stats 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.
Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.
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cohortcalls cohortmodel casecalls 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.
Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
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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.
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)
GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).
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genes features clusters gbk json versions
Biosynthetic Gene Cluster prediction with Conditional Random Fields.
Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach
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linear_plot_png transformed_linear_plot_png log_plot_png transformed_log_plot_png model summary lookup_table fitted_histogram_png versions
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
GenomeTools gt-stat utility to show statistics about features contained in GFF3 files
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stats 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
Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes
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db versions
Python package for detection of chimerism and contamination in prokaryotic genomes.
Merging of CheckM and GUNC results in one summary table
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tsv versions
Python package for detection of chimerism and contamination in prokaryotic genomes.
Detection of Chimerism and Contamination in Prokaryotic Genomes
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maxcss_level_tsv all_levels_tsv versions
Python package for detection of chimerism and contamination in prokaryotic genomes.
Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides users a graphical report to investigate the contamination further. Internally, it uses the Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.
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txt html versions
Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.
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summary_csv roc_all_csv roc_indel_locations_csv roc_indel_locations_pass_csv roc_snp_locations_csv roc_snp_locations_pass_csv extended_csv runinfo metrics_json vcf tbi versions
Haplotype VCF comparison tools
Whole-genome assembly using PacBio HiFi reads
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raw_unitigs bin_files processed_unitigs primary_contigs alternate_contigs hap1_contigs hap2_contigs corrected_reads read_overlaps log versions
gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference
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wig versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline
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vcf versions
Human mitochondrial variants annotation using HmtVar.
write your description here
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fastq json versions
Hostile: accurate host decontamination
Downloads required reference genomes for Hostile
NO input
reference versions
Hostile: accurate host decontamination
A Python application to generate self-contained HTML reports for variant review and other genomic applications
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report versions
Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.
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mask versions
Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.
Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.
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output versions
Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.
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
Generate a consensus sequence from a BAM file using iVar
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fasta qual mpileup versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Trim primer sequences rom a BAM file with iVar
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bam log versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Call variants from a BAM file using iVar
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tsv mpileup versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)
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bed versions
Java utilities for Bioinformatics.
Removes low abundance k-mers from FASTA/FASTQ files
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trimmed versions
khmer k-mer counting library
A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.
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smorfs all_orfs amp_prediction readme_file log_file versions
A pipeline for AMP (antimicrobial peptide) prediction
MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
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index versions log
A tool for mapping metagenomic data
MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
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rma6 alignments log versions
A tool for mapping metagenomic data
Screens query sequences against large sequence databases
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screen versions
Fast sequence distance estimator that uses MinHash
MaxBin is a software that is capable of clustering metagenomic contigs
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binned_fastas summary abundance log marker_counts unbinned_fasta tooshort_fasta marker_bins marker_genes versions
Analyses a DAA file and exports information in text format
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txt_gz megan versions
A tool for studying the taxonomic content of a set of DNA reads
Analyses an RMA file and exports information in text format
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txt megan_summary versions
A tool for studying the taxonomic content of a set of DNA reads
Compare k-mer frequency in reads and assembly to devise the metrics K and QV
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hist log_stderr versions
Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of Merqury) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads.
A reimplemenation of KatGC to work with FastK databases
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filled_gc_plot line_gc_plot stacked_gc_plot versions
FastK based version of Merqury
FastK based version of Merqury
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stats bed assembly_qv spectra_cn_fl spectra_cn_ln spectra_cn_st qv spectra_asm_fl spectra_asm_ln spectra_asm_st phased_block_bed phased_block_stats continuity_N block_N block_blob hapmers_blob versions
FastK based version of Merqury
Depth computation per contig step of metabat2
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depth versions
Metagenome binning of contigs
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tooshort lowdepth unbinned membership fasta versions
Strain-level metagenomic assignment
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wimp evidence_unknown_species reads2taxon em contig_coverage length_and_id krona versions
Metagenome assembler for long-read sequences (HiFi and ONT).
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contigs log versions
MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
Minia is a short-read assembler based on a de Bruijn graph
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contigs unitigs h5 versions
A tool for quality control and tracing taxonomic origins of microRNA sequencing data
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html json tsv all_fa rnatype_unknown_fa versions
miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.
A python workflow that assembles mitogenomes from Pacbio HiFi reads
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fasta stats gb gff all_potential_contigs contigs_annotations contigs_circularization contigs_filtering coverage_mapping coverage_plot final_mitogenome_annotation final_mitogenome_choice final_mitogenome_coverage potential_contigs reads_mapping_and_assembly shared_genes versions
A python workflow that assembles mitogenomes from Pacbio HiFi reads
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.
A bioinformatics tool for working with modified bases
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bed bedgraph log versions
A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data
Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.
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img_clahe versions
One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines.
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.
Run NanoPlot on nanopore-sequenced reads
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html png txt log versions
NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose
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vecscreen_output versions
"NCBI libraries for biology applications (text-based utilities)"
Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.
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pt versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.
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pdf corr_matrix all matched versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates
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index versions
Alignment with PacBio's minimap2 frontend
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bam versions
A minimap2 frontend for PacBio native data formats
Creates a sequence dictionary for a reference sequence.
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reference_dict versions
Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
Generate GWAS association studies
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assoc log nosex versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
pmdtools command to filter ancient DNA molecules from others
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bam versions
Compute postmortem damage patterns and decontaminate ancient genomes
Polishing genome assemblies with short reads.
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fasta versions debug
Polishing genome assemblies with short reads.
Extension of Porechop whose purpose is to process adapter sequences in ONT reads.
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reads log versions
converts sam/bam/cram/pairs into genome contact map
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pretext versions
a module to generate images from Pretext contact maps.
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image versions
Compute summary statistics for control gene from BAM files.
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control_stats versions
A Python package for pharmacogenomics research
Evaluate alignment data
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results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Evaluate alignment data
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results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Evaluate alignment data
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results versions
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Interface and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.
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junc versions
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
Predict antibiotic resistance from protein or nucleotide data
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json tsv tmp tool_version db_version versions
This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
Quality control of riboseq bam data
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predictions all transprofile versions
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
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.
This module combines samtools and samblaster in order to use samblaster capability to filter or tag SAM files, with the advantage of maintaining both input and output in BAM format. Samblaster input must contain a sequence header: for this reason it has been piped with the "samtools view -h" command. Additional desired arguments for samtools can be passed using: options.args2 for the input bam file options.args3 for the output bam file
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bam versions
List CRAM Content-ID and Data-Series sizes
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size versions
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.
Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.
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bam cram sam versions
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.
Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.
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orientation_data contamination_data contamination_segments stats vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Generates a BED file containing genomic locations of lengths of N.
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bed versions
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
Sequence quality metrics for FASTQ and uBAM files.
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json html versions
Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
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seqz versions
Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
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
Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2.
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phased_variant versions
Fast and accurate method for estimation of haplotypes (phasing)
validate consistency of feature and sample annotations with matrices and contrasts
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sample_meta feature_meta assays contrasts versions
Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.
Simple ANI calculation between reference and query genomes.
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dist versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Memory-efficient ANI database queries with skani.
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search versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
Storing skani sketches/indices on disk.
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sketch_dir sketch markers versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
All-to-all ANI computation.
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triangle versions
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
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
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
Compare many FracMinHash signatures generated by sourmash sketch.
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matrix labels csv versions
Compute and compare FracMinHash signatures for DNA and protein data sets.
Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.
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result unassigned matches prefetch prefetchcsv versions
Compute and compare FracMinHash signatures for DNA data sets.
Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.
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result versions
Compute and compare FracMinHash signatures for DNA data sets.
Assembles a small genome (bacterial, fungal, viral)
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scaffolds contigs transcripts gene_clusters gfa warnings log versions
Fast, efficient, lossless compression of FASTQ files.
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spring versions
SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)
Fast, efficient, lossless decompression of FASTQ files.
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fastq versions
SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)
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.
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
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results_xlsx summary_tsv detailed_summary_tsv resfinder_tsv plasmidfinder_tsv mlst_tsv settings_txt pointfinder_tsv versions
Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.
SummarizedExperiment container
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rds log versions
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Converts VCFs containing structural variants to BED format
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bed versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Parses a Thermo RAW file containing mass spectra to an open file format
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spectra versions
Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle
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classifications log fasta versions
Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.
A post sequencing QC tool for Oxford Nanopore sequencers
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report_data report_html plots_html plotly_js versions
Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
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bam log tsv_edit_distance tsv_per_umi tsv_umi_per_position versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
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reads log versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Group reads based on their UMI and mapping coordinates
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log bam tsv versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Make the output from umi_tools dedup or group compatible with RSEM
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bam log versions
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing
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bcf_gz vcf_gz bcf vcf versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
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.
Obtains per-sample observations for the actual calling process with varlociraptor calls
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bcf_gz vcf_gz bcf vcf versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
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.
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.
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.
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)
a pangenome-scale aligner
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paf versions
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.
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