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.
The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will automatically remove this feature too.
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gff
versions
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
Run the alignment/variant-call/consensus logic of the artic pipeline
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results
bam
bai
bam_trimmed
bai_trimmed
bam_primertrimmed
bai_primertrimmed
fasta
vcf
tbi
json
versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
generate VCF file from a BAM file using various calling methods
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vcf
versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.
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vcf
tbi
csi
versions
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Concatenate VCF files
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vcf
tbi
csi
versions
Concatenate VCF files.
Compresses VCF files
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fasta
versions
Create consensus sequence by applying VCF variants to a reference fasta file.
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.
bcftools Haplotype-aware consequence caller
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vcf
tbi
csi
versions
Haplotype-aware consequence caller
Filters VCF files
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vcf
tbi
csi
versions
Apply fixed-threshold filters to VCF files.
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.
Apply set operations to VCF files
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results
versions
Computes intersections, unions and complements of VCF files.
Merge VCF files
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vcf
index
versions
Merge VCF files.
Compresses VCF files
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vcf
tbi
stats
mpileup
versions
Generates genotype likelihoods at each genomic position with coverage.
Normalize VCF file
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vcf
tbi
csi
versions
Normalize VCF files.
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.
Extracts fields from VCF or BCF files and outputs them in user-defined format.
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output
versions
Extracts fields from VCF or BCF files and outputs them in user-defined format.
Sorts VCF files
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vcf
tbi
csi
versions
Sort VCF files by coordinates.
Generates stats from VCF files
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stats
versions
Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
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vcf
tbi
csi
versions
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF 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.
Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
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genomecov
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
extract sequences in a FASTA file based on intervals defined in a feature file.
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fasta
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Groups features in a BED file by given column(s) and computes summary statistics for each group to another column.
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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.
Allows one to screen for overlaps between two sets of genomic features.
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intersect
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Calculate Jaccard statistic b/w two feature files.
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tsv
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Makes adjacent or sliding windows across a genome or BED 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.
masks sequences in a FASTA file based on intervals defined in a feature file.
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fasta
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
combines overlapping or โbook-endedโ features in an interval file into a single feature which spans all of the combined features.
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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.
Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.
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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.
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.
Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
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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.
Sorts a feature file by chromosome and other criteria.
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sorted
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
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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.
Combines multiple BedGraph files into a single 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.
Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
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vcf
versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Performs alignment of BS-Seq reads using bismark
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bam
report
unmapped
versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
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.
Removes alignments to the same position in the genome from the Bismark mapping output.
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bam
report
versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.
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index
versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Extracts methylation information for individual cytosines from alignments.
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1
bedgraph
methylation_calls
coverage
report
mbias
versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Collects bismark alignment reports
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report
versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report.
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summary
versions
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.
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reference
versions
Cell Ranger processes data from 10X Genomics Chromium kits. cellranger vdj
takes FASTQ files from cellranger mkfastq
or bcl2fastq
for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe
file which can be loaded into Loupe V(D)J Browser.
Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.
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outs
versions
Cell Ranger processes data from 10X Genomics Chromium kits. cellranger vdj
takes FASTQ files from cellranger mkfastq
or bcl2fastq
for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe
file which can be loaded into Loupe V(D)J Browser.
Given segmented log2 ratio estimates (.cns), derive each segmentโs absolute integer copy number
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cns
versions
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.
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root
tab
versions
Tool for calling copy number variations.
convert2vcf.pl is command line tool to convert CNVnator calls to vcf format.
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vcf
versions
Tool for calling copy number variations.
Command line tool for calling CNVs in whole genome sequencing data
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pytor
versions
calling CNVs using read depth
calculates read depth histograms
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pytor
versions
calling CNVs using read depth
command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.
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pytor
versions
calling CNVs using read depth
partitioning read depth histograms
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pytor
versions
calling CNVs using read depth
view function to generate vcfs
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vcf
tsv
xls
versions
calling CNVs using read depth
structural-variant calling with cutesv
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vcf
versions
DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.
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vcf
vcf_tbi
gvcf
gvcf_tbi
versions
(DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf
vcf_tbi
gvcf
gvcf_tbi
versions
Call variants from the examples produced by make_examples
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call_variants_tfrecords
versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
Transforms the input alignments to a format suitable for the deep neural network variant caller
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examples
gvcf
versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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1
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vcf
vcf_tbi
gvcf
gvcf_tbi
versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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1
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1
vcf
vcf_tbi
gvcf
gvcf_tbi
versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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report
versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
Call structural variants
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bcf
csi
versions
Structural variant discovery by integrated paired-end and split-read analysis
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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5
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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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2
vcf
tbi
versions
Convert a file in FASTA format to the ELFASTA format
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elfasta
log
versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.
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6
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1
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1
0
0
0
0
0
bam
logs
metrics
recall
gvcf
table
activity_profile
assembly_regions
versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Merge split bam/sam chunks in one file
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bam
versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Split bam file into manageable chunks
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bam
versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule.
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0
0
bam
versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
Calls consensus sequences from reads with the same unique molecular tag.
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0
0
bam
versions
Tools for working with genomic and high throughput sequencing data.
Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.
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1
0
0
0
bam
versions
A set of tools for working with genomic and high throughput sequencing data, including UMIs
A haplotype-based variant detector
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5
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1
vcf
versions
call variant and sequencing depth information of the variant
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0
variants
versions
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
Gene Allele Mutation Microbial Assessment
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0
gamma
psl
gff
fasta
versions
Tool for Gene Allele Mutation Microbial Assessment
Performs local realignment around indels to correct for mapping errors
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1
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1
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0
1
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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1
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1
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1
0
1
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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1
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1
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1
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1
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1
0
1
vcf
versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the first step by VariantRecalibrator and a target sensitivity value.
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4
5
0
0
0
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.
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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2
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.
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
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1
2
0
0
0
combined_gvcf
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.
Determines the baseline contig ploidy for germline samples given counts data
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3
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1
0
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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2
3
4
5
6
7
0
1
0
1
0
1
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.
Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
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3
4
0
1
0
1
0
1
0
1
0
1
vcf
tbi
versions
Genome Analysis Toolkit (GATK4)
Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.
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3
4
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.
Call germline SNPs and indels via local re-assembly of haplotypes
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3
4
0
1
0
1
0
1
0
1
0
1
vcf
tbi
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.
Call somatic SNVs and indels via local assembly of haplotypes.
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1
2
3
0
1
0
1
0
1
0
0
0
0
vcf
tbi
stats
f1r2
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.
Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
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1
2
3
intervals
segments
denoised
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.
Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
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1
2
0
peak
versions
bedgraph_pvalues
bedgraph_pileup
bed_intervals
duplicates
Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.
0
1
2
3
4
5
6
7
0
0
0
errors_cal
errors_grp
errors_spl
rsquare_grp
rsquare_spl
versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
Generates haplotype calls by sampling haplotype estimates
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1
haplo_sampled
versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
merge gVCF files and perform joint variant calling
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1
0
1
bcf
versions
Tools for population-scale genotyping using pangenome graphs.
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1
vcf
tbi
versions
A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.
Call variants from a BAM file using iVar
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1
0
0
0
0
tsv
mpileup
versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Filtering VCF with dynamically-compiled java expressions
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1
2
3
0
1
0
1
0
1
0
1
0
1
vcf
tbi
csi
versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
quantifies scRNA-seq data from fastq files using kb-python.
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1
0
0
0
0
0
0
count
versions
matrix
kallisto and bustools are wrapped in an easy-to-use program called kb
Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.
0
0
0
reads
versions
khmer k-mer counting library
Lofreq subcommand to for insert base and indel alignment qualities
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1
0
bam
versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments
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1
2
0
vcf
versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
It predicts variants using multiple processors
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1
2
3
0
1
0
1
vcf
tbi
versions
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors
Lofreq subcommand to remove variants with low coverage or strand bias potential
0
1
vcf
versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Inserts indel qualities in a BAM file
0
1
0
1
bam
versions
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
0
1
2
3
4
5
0
1
0
1
vcf
versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
0
1
0
1
bam
versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
0
1
2
0
peak
xls
versions
gapped
bed
bdg
Model Based Analysis for ChIP-Seq data
Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
0
1
2
0
peak
xls
versions
gapped
bed
bdg
Model Based Analysis for ChIP-Seq 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.
0
1
0
1
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.
0
1
2
3
4
0
1
0
1
0
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.
0
1
2
3
4
5
6
0
1
0
1
0
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.
0
1
2
3
4
0
1
0
1
0
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
Extracts per-base methylation metrics from alignments
0
1
2
0
0
bedgraph
methylkit
versions
Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.
A tool for quality control and tracing taxonomic origins of microRNA sequencing data
0
1
2
0
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.
Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
0
0
dataset
versions
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
0
1
0
csv
csv_errors
csv_insertions
tsv
json
json_auspice
ndjson
fasta_aligned
fasta_translation
nwk
versions
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Calls CNVs in bam files from tumor patients
0
1
2
3
4
0
0
png
profile
summary
versions
NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database
0
1
2
3
vcf
versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.
0
1
2
3
0
1
vcf
gvcf
versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.
0
1
2
3
0
1
vcf
versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
pbsv - PacBio structural variant (SV) signature discovery tool
0
1
0
1
svsig
versions
pbsv - PacBio structural variant (SV) calling and analysis tools
Automatically improve draft assemblies and find variation among strains, including large event detection
0
1
0
1
2
0
improved_assembly
vcf
change_record
tracks_bed
tracks_wig
versions
Main caller script for peak calling
0
1
2
0
divergent_TREs
bidirectional_TREs
unidirectional_TREs
peakcalling_log
versions
Peak Identifier for Nascent Transcripts Starts (PINTS)
PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.
0
1
0
1
0
1
2
vcf
max_cov
bad_sites
versions
Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to 'link'.
0
1
2
0
txt
png
loess_qc_txt
loess_txt
versions
Copy number calling and SNV classification using targeted short read sequencing
Generate on and off-target intervals for PureCN from a list of targets
0
1
0
1
0
txt
bed
versions
Copy number calling and SNV classification using targeted short read sequencing
Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.
0
1
2
3
0
0
rds
png
bias_rds
bias_bed
low_cov_bed
versions
Copy number calling and SNV classification using targeted short read sequencing
Run PureCN workflow to normalize, segment and determine purity and ploidy
0
1
2
0
0
pdf
local_optima_pdf
seg
genes_csv
amplification_pvalues_csv
vcf_gz
variants_csv
loh_csv
chr_pdf
segmentation_pdf
multisample_seg
versions
Copy number calling and SNV classification using targeted short read sequencing
Call SNVs/indels from BAM files for all target genes.
0
1
2
0
1
0
0
vcf
tbi
versions
A Python package for pharmacogenomics research
PyPGx pharmacogenomics genotyping pipeline for NGS data.
0
1
2
3
4
5
0
1
0
results
cnv_calls
consolidated_variants
versions
A Python package for pharmacogenomics research
Markup VCF file using rho-calls.
0
1
2
0
1
0
vcf
versions
Call regions of homozygosity and make tentative UPD calls.
Call regions of homozygosity and make tentative UPD calls
0
1
0
1
bed
wig
versions
Call regions of homozygosity and make tentative UPD calls.
The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
0
1
2
3
4
5
6
0
1
tp_vcf
tp_tbi
fn_vcf
fn_tbi
fp_vcf
fp_tbi
baseline_vcf
baseline_tbi
snp_roc
non_snp_roc
weighted_roc
summary
phasing
versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
0
1
2
0
csv
json
bam
versions
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
Call peaks using SEACR on sequenced reads in bedgraph format
0
1
2
0
bed
versions
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).
Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm
0
1
2
3
4
5
0
1
0
1
vcf
tbi
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.
Create BWA index for reference genome
0
1
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.
Performs fastq alignment to a fasta reference using Sentieon's BWA MEM
0
1
0
1
0
1
0
1
bam_and_bai
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.
Accelerated implementation of the Picard CollectVariantCallingMetrics tool.
0
1
2
0
1
2
0
1
0
1
0
1
metrics
summary
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.
Accelerated implementation of the GATK DepthOfCoverage tool.
0
1
2
0
1
0
1
0
1
0
1
per_locus
sample_summary
statistics
coverage_counts
coverage_proportions
interval_summary
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.
Collects multiple quality metrics from a bam file
0
1
2
0
1
0
1
0
mq_metrics
qd_metrics
gc_summary
gc_metrics
aln_metrics
is_metrics
mq_plot
qd_plot
is_plot
gc_plot
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.
Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.
0
1
2
0
1
0
1
cram
crai
bam
bai
score
metrics
metrics_multiqc_tsv
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.
modifies the input VCF file by adding the MLrejected FILTER to the variants
0
1
2
0
1
0
1
0
1
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.
DNAscope algorithm performs an improved version of Haplotype variant calling.
0
1
2
3
0
1
0
1
0
1
0
1
0
1
0
0
0
vcf
vcf_tbi
gvcf
gvcf_tbi
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.
Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.
0
1
2
3
0
1
0
1
0
1
0
1
vcf_gz
vcf_gz_tbi
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.
Runs Sentieon's haplotyper for germline variant calling.
0
1
2
3
4
0
1
0
1
0
1
0
1
0
0
vcf
vcf_tbi
gvcf
gvcf_tbi
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.
Generate recalibration table and optionally perform base quality recalibration
0
1
2
0
1
0
1
0
1
0
1
0
1
0
table
table_post
recal_alignment
csv
pdf
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.
Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.
0
1
2
0
1
0
1
output
index
output_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.
Filters the raw output of sentieon/tnhaplotyper2.
0
1
2
3
4
5
6
0
1
0
1
vcf
vcf_tbi
stats
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.
Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.
0
1
2
3
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
0
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.
TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.
0
1
2
0
1
0
1
0
1
2
0
1
2
0
1
2
0
1
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.
Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR). VarCal builds a recalibration model for scoring variant quality. https://support.sentieon.com/manual/usages/general/#varcal-algorithm
0
1
2
0
0
0
0
0
recal
idx
tranches
plots
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.
Collects whole genome quality metrics from a bam file
0
1
2
0
1
0
1
0
1
wgs_metrics
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.
PileupCaller is a tool to create genotype calls from bam files using read-sampling methods
0
1
0
0
eigenstrat
plink
freqsum
versions
Tools for population genetics on sequencing data
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
0
1
2
3
4
5
0
1
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
Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.
0
1
2
merged_variants
versions
Fast and accurate method for estimation of haplotypes (phasing)
Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.
0
1
2
3
4
0
1
2
0
1
2
0
1
phased_variant
versions
Fast and accurate method for estimation of haplotypes (phasing)
tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2ฮ7โ8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.
0
1
2
smncopynumber
run_metrics
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.
0
1
2
3
0
1
0
1
vcf
versions
structural variant calling and genotyping with existing tools, but, smoothly
structural-variant calling with sniffles
0
1
2
0
1
0
1
0
0
vcf
tbi
snf
versions
Core-SNP alignment from Snippy outputs
0
1
2
0
aln
full_aln
tab
vcf
txt
versions
Rapid bacterial SNP calling and core genome alignments
Rapid haploid variant calling
0
1
0
tab
csv
html
vcf
bed
gff
bam
bai
log
aligned_fa
consensus_fa
consensus_subs_fa
raw_vcf
filt_vcf
vcf_gz
vcf_csi
txt
versions
Rapid bacterial SNP calling and core genome alignments
Annotate a VCF file with another VCF file
0
1
2
0
1
2
vcf
versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
The dbNSFP is an integrated database of functional predictions from multiple algorithms
0
1
2
0
1
2
vcf
versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
0
1
0
1
2
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
0
1
2
0
1
0
1
0
1
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
0
1
2
0
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
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
0
1
2
3
4
0
0
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
0
1
2
3
4
5
6
7
8
0
0
vcf_indels
vcf_indels_tbi
vcf_snvs
vcf_snvs_tbi
versions
Strelka calls somatic and germline small variants from mapped sequencing reads
SummarizedExperiment container
0
1
0
1
0
1
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.
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
0
1
2
3
4
0
1
0
1
0
1
0
1
0
1
0
1
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
Convert SV calls to a standardized format.
0
1
0
standardized_vcf
versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
A tool to standardize VCF files from structural variant callers
0
1
2
3
vcf
versions
Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA
0
1
csv_gz
versions
Computes the coverage of different regions from the bam file.
0
1
0
1
cov
wig
versions
TIDDIT - structural variant calling.
Given baseline and comparison sets of variants, calculate the recall/precision/f-measure
0
1
2
3
4
5
0
1
0
1
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
Simple software to call UPD regions from germline exome/wgs trios.
0
1
bed
versions
The Java port of the VarDict variant caller
0
1
2
3
0
1
0
1
vcf
versions
Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing
0
1
2
0
0
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.
0
1
0
1
0
1
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
0
1
2
3
4
0
1
0
1
bcf_gz
vcf_gz
bcf
vcf
versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Constructs a graph from a reference and variant calls or a multiple sequence alignment file
0
1
2
3
0
1
0
1
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
0
1
0
0
vcf
versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
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xg
vg_index
versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
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.
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
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