Programs for NGS work

Application purpose Name Short description Links
ChIP-SeqMACS2Model-based Analysis of ChIP-Seq data for identifying transcript factor binding siteshomepage
DNAABySSparallel assembler for short read sequence datapublication, tutorial
ALLPATHS-LGshort read genome assemblerhomepage, tutorial
AMOSmodular open source whole genome assemblerpublication, tutorial
BamToolscommand-line toolkit for for handling genome alignment filestutorial
BBMapa splice-aware global aligner for DNA and RNA sequencing readshomepage, tutorial
BCFtoolsutilities for variant calling and manipulating VCFs and BCFshomepage, tutorial
bcl2fastqdemultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formatshomepage
BESSTscaffolding of large fragmented assembliespublication, tutorial
Bowtie 1ultrafast, memory-efficient short read alignerhomepage
Bowtie 2ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequenceshomepage
BUSCOquantitative measures for the assessment of genome assembly, gene set, and transcriptome completenesshomepage, publication
Burrows-Wheeler Alignersoftware package for mapping low-divergent sequences against a large reference genomehomepage
CanuCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).documentation
Celera Assemblerde novo whole-genome shotgun (WGS) DNA sequence assemblerhomepage
Cutadaptsearches for the adapter in all reads and removes it when foundpublication, tutorial
deepToolscommand-line tools to process and analyze deep sequencing datahomepage
eXpressstreaming fragment assignment and quantification for high-throughput sequencinghomepage
FastQCquality control tool for high throughput sequence datahomepage
FASTXcollection of command line tools for Short-Reads FASTA/FASTQ files preprocessinghomepage
GapFillerstand-alone program for closing gaps within pre-assembled scaffoldspublication
GATKtoolkit for variant discovery in high-throughput sequencing datahomepage
Geneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
HOMERsuite of tools for Motif Discovery and next generation sequencing analysishomepage
HTSeqPython package that provides infrastructure to process data from high-throughput sequencing assayspublication, homepage
IDBAde novo assembler for short reads sequencing data with highly uneven sequencing depthshomepage
JMP Genomicsadvanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle)homepage
LoRDECLoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.homepage
MARVELMARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.homepage
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequenceshomepage, publication, manual
MIRAa multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNA-seq projectshomepage
ngs.plota standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on NGS data.publication
PauvreQC and genome browser plotting Oxford Nanopore and PacBio long readshomepage
Picardset of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCFhomepage
PlatanusPLATform for Assembling NUcleotide Sequences is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing datahomepage, publication
POPBAMtools for evolutionary analysis of short read sequence alignmentspublication
Porechopadapter trimmer for Oxford Nanopore readshomepage
poretoolstoolkit for working with nanopore sequencing data from Oxford Nanoporehomepage
Raconultrafast consensus module for raw de novo genome assembly of long uncorrected readspublication, tutorial
SMARTdenovoUltra-fast de novo assembler using long noisy reads.homepage
SOAPaligneralignment toolhomepage
SOAPdenovode novo short reads assemblerhomepage
SortMeRNAa program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic datahomepage
SRA-Toolkittoolkit to convert .sra files into other formatspublication
SSPACE-LongReada program for scaffolding longreads (e.g. PacBio RS reads)homepage, publication
SSPACE-Standarda program for scaffolding pre-assembled contigs using NGS paired-read datahomepage, publication
Stackssoftware pipeline for building loci from short-read sequenceshomepage, publication
Staden Packagetools for DNA sequence assembly, editing and sequence analysishomepage
SVDetectSVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data.homepage, manual
Velvetsequence assembler for very short readshomepage
Hi-CHiC-ProHiC-Pro: An optimized and flexible pipeline for Hi-C data processing documentation, publication
hichipperhichipper is a command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data.homepage, documentation
RADseqipyradinteractive assembly and analysis of RADseq data setsdocumentation
pyRADassembly of de novo RADseq loci for phylogenetic analysespublication
RNABBMapa splice-aware global aligner for DNA and RNA sequencing readshomepage, tutorial
BinPackerpacking-based de novo transcriptome assembly from RNA-seq datapublication
BUSCOquantitative measures for the assessment of genome assembly, gene set, and transcriptome completenesshomepage, publication
Cell RangerA set of analysis pipelines that process Chromium single cell 3' RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. For viewer software, see Loupe Cell Browser.homepage
Cufflinksassembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq sampleshomepage
Cutadaptsearches for the adapter in all reads and removes it when foundpublication, tutorial
deepToolscommand-line tools to process and analyze deep sequencing datahomepage
DESeqdifferential gene expression of RNA-seq data at the gene levelpublication, homepage
DETONATEde novo transcriptome RNA-seq assemblyhomepage
DEXSeqpackage for finding differential exon usage using RNA-seq exon countspublication, homepage
exomePeakexome-based analysis for RNA epigenome sequencing datapublication, homepage
FastQCquality control tool for high throughput sequence datahomepage
FASTXcollection of command line tools for Short-Reads FASTA/FASTQ files preprocessinghomepage
Geneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
HTSeqPython package that provides infrastructure to process data from high-throughput sequencing assayspublication, homepage
JMP Genomicsadvanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle)homepage
kallistoprogram for quantifying abundances of transcripts from RNA-Seq datahomepage, publication
KisSplicelocal transcriptome assembler for SNPs, indels and AS eventshomepage
Loupe Cell BrowserA desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium Single Cell 5' and 3' gene expression data.homepage
MarkerMinerfully automated workflow and application for discovery of SCN loci in angiospermshomepage, publication
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequenceshomepage, publication, manual
miRDeep2A tool for discovering known and novel miRNAs from small RNA sequencing data.documentation, publication, tutorial
miRExpresstool to analyze high-throughput sequencing data for profiling microRNA expressionhomepage, publication
mirPRoa novel standalone program for differential expression and variation analysis of miRNAshomepage, publication
Oasesde novo transciptome assembler for very short readshomepage, publication
RSEMaccurate transcript quantification from RNA-Seq data with or without a reference genomepublication
RSeQCa package that provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq datahomepage
SalmonA tool for quantifying the expression of transcripts using RNA-seq data.homepage
ScallopScallop is a reference-based transcriptome assembler for RNA-seq.homepage, publication
SNPiRa suite of tools for reliable identification of genomic variants using RNA-seq datapublication
SOAPdenovo-TransA de novo transcriptome assembler designed specifically for RNA-Seq.homepage, publication
SortMeRNAa program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic datahomepage
STARSpliced Transcript Alignment to a Reference: fast RNA-seq read mapperhomepage
TopHatfast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using Bowtiehomepage
Trans-ABySSde novo assemly of RNA-Seq datahomepage, publication
Transratesoftware for de-novo transcriptome assembly quality analysishomepage
TRINITYde novo reconstruction of transcriptomes from RNA-Seq datahomepage, publication
SNPSNPiRa suite of tools for reliable identification of genomic variants using RNA-seq datapublication
SubreadHigh-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP.homepage
alignmentBamToolscommand-line toolkit for for handling genome alignment filestutorial
analysisCell RangerA set of analysis pipelines that process Chromium single cell 3' RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. For viewer software, see Loupe Cell Browser.homepage
Cufflinksassembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq sampleshomepage
deepToolscommand-line tools to process and analyze deep sequencing datahomepage
DESeqdifferential gene expression of RNA-seq data at the gene levelpublication, homepage
exomePeakexome-based analysis for RNA epigenome sequencing datapublication, homepage
Geneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
HailHail is an open-source, scalable framework for exploring and analyzing genomic data.homepage
HOMERsuite of tools for Motif Discovery and next generation sequencing analysishomepage
ipyradinteractive assembly and analysis of RADseq data setsdocumentation
kallistoprogram for quantifying abundances of transcripts from RNA-Seq datahomepage, publication
KatualiKatuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data.homepage, documentation
Loupe Cell BrowserA desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium Single Cell 5' and 3' gene expression data.homepage
MACS2Model-based Analysis of ChIP-Seq data for identifying transcript factor binding siteshomepage
MarkerMinerfully automated workflow and application for discovery of SCN loci in angiospermshomepage, publication
miRDeep2A tool for discovering known and novel miRNAs from small RNA sequencing data.documentation, publication, tutorial
miRExpresstool to analyze high-throughput sequencing data for profiling microRNA expressionhomepage, publication
mirPRoa novel standalone program for differential expression and variation analysis of miRNAshomepage, publication
PomoxisPomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.documentation
RSEMaccurate transcript quantification from RNA-Seq data with or without a reference genomepublication
SalmonA tool for quantifying the expression of transcripts using RNA-seq data.homepage
SNPiRa suite of tools for reliable identification of genomic variants using RNA-seq datapublication
Staden Packagetools for DNA sequence assembly, editing and sequence analysishomepage
annotationHailHail is an open-source, scalable framework for exploring and analyzing genomic data.homepage
assemblyABySSparallel assembler for short read sequence datapublication, tutorial
ALLPATHS-LGshort read genome assemblerhomepage, tutorial
AMOSmodular open source whole genome assemblerpublication, tutorial
BinPackerpacking-based de novo transcriptome assembly from RNA-seq datapublication
CanuCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).documentation
Celera Assemblerde novo whole-genome shotgun (WGS) DNA sequence assemblerhomepage
Cufflinksassembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq sampleshomepage
DETONATEde novo transcriptome RNA-seq assemblyhomepage
Geneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
IDBAde novo assembler for short reads sequencing data with highly uneven sequencing depthshomepage
ipyradinteractive assembly and analysis of RADseq data setsdocumentation
KisSplicelocal transcriptome assembler for SNPs, indels and AS eventshomepage
MARVELMARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.homepage
MiniasmUltrafast de novo assembly for long noisy reads (though having no consensus step) homepage
MIRAa multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNA-seq projectshomepage
NanopolishSoftware package for signal-level analysis of Oxford Nanopore sequencing datamanual
Oasesde novo transciptome assembler for very short readshomepage, publication
PilonPilon is an automated genome assembly improvement and variant detection tool.homepage
PlatanusPLATform for Assembling NUcleotide Sequences is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing datahomepage, publication
pyRADassembly of de novo RADseq loci for phylogenetic analysespublication
Raconultrafast consensus module for raw de novo genome assembly of long uncorrected readspublication, tutorial
ScallopScallop is a reference-based transcriptome assembler for RNA-seq.homepage, publication
SMARTdenovoUltra-fast de novo assembler using long noisy reads.homepage
SOAPdenovode novo short reads assemblerhomepage
SOAPdenovo-TransA de novo transcriptome assembler designed specifically for RNA-Seq.homepage, publication
Staden Packagetools for DNA sequence assembly, editing and sequence analysishomepage
Trans-ABySSde novo assemly of RNA-Seq datahomepage, publication
Transratesoftware for de-novo transcriptome assembly quality analysishomepage
TRINITYde novo reconstruction of transcriptomes from RNA-Seq datahomepage, publication
Velvetsequence assembler for very short readshomepage
wtdbg2A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.homepage
countingSubreadHigh-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP.homepage
filter/trimmingCutadaptsearches for the adapter in all reads and removes it when foundpublication, tutorial
FiltlongFiltlong is a tool for filtering long reads by quality.homepage
NanofiltFiltering and trimming of long read sequencing datahomepage, publication
Porechopadapter trimmer for Oxford Nanopore readshomepage
SortMeRNAa program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic datahomepage
Trim Galore!wrapper tool around Cutadapt and FastGC to consistently apply quality and adapter trimming to FastQ fileshomepage
Trimmomaticflexible trimmer for Illumina NGS datahomepage
genome browserPauvreQC and genome browser plotting Oxford Nanopore and PacBio long readshomepage
genomicsJMP Genomicsadvanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle)homepage
molecular biologyGeneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
nanopore sequencingCanuCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).documentation
Flappie Flip-flop basecaller for Oxford Nanopore reads.homepage
GuppyAccelerated basecaller for Oxford Nanopore Sequencinghomepage
KatualiKatuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data.homepage, documentation
MARVELMARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.homepage
MedakaMedaka is a tool to create a consensus sequence from nanopore sequencing data.homepage, documentation
MiniasmUltrafast de novo assembly for long noisy reads (though having no consensus step) homepage
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequenceshomepage, publication, manual
NanofiltFiltering and trimming of long read sequencing datahomepage, publication
NanopolishSoftware package for signal-level analysis of Oxford Nanopore sequencing datamanual
NanoStatCreate statistic summary of an Oxford Nanopore read datasethomepage, publication
PauvreQC and genome browser plotting Oxford Nanopore and PacBio long readshomepage
PomoxisPomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.documentation
Porechopadapter trimmer for Oxford Nanopore readshomepage
poretoolstoolkit for working with nanopore sequencing data from Oxford Nanoporehomepage
ScrappieBasecaller for Oxford Nanopore Sequencinghomepage
SMARTdenovoUltra-fast de novo assembler using long noisy reads.homepage
wtdbg2A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.homepage
phylogeneticsfastStructureA variational framework for inferring population structure from SNP genotype data.homepage, publication
MarkerMinerfully automated workflow and application for discovery of SCN loci in angiospermshomepage, publication
POPBAMtools for evolutionary analysis of short read sequence alignmentspublication
pyRADassembly of de novo RADseq loci for phylogenetic analysespublication
quality controlBUSCOquantitative measures for the assessment of genome assembly, gene set, and transcriptome completenesshomepage, publication
FastQCquality control tool for high throughput sequence datahomepage
HailHail is an open-source, scalable framework for exploring and analyzing genomic data.homepage
hichipperhichipper is a command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data.homepage, documentation
LoRDECLoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.homepage
QUASTQUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.Homepage, manual
RSeQCa package that provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq datahomepage
Transratesoftware for de-novo transcriptome assembly quality analysishomepage
Trim Galore!wrapper tool around Cutadapt and FastGC to consistently apply quality and adapter trimming to FastQ fileshomepage
scaffoldingBESSTscaffolding of large fragmented assembliespublication, tutorial
GapFillerstand-alone program for closing gaps within pre-assembled scaffoldspublication
SSPACE-LongReada program for scaffolding longreads (e.g. PacBio RS reads)homepage, publication
SSPACE-Standarda program for scaffolding pre-assembled contigs using NGS paired-read datahomepage, publication
sequence alignmentBBMapa splice-aware global aligner for DNA and RNA sequencing readshomepage, tutorial
Bowtie 1ultrafast, memory-efficient short read alignerhomepage
Bowtie 2ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequenceshomepage
Burrows-Wheeler Alignersoftware package for mapping low-divergent sequences against a large reference genomehomepage
Cell RangerA set of analysis pipelines that process Chromium single cell 3' RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. For viewer software, see Loupe Cell Browser.homepage
Geneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequenceshomepage, publication, manual
SOAPaligneralignment toolhomepage
STARSpliced Transcript Alignment to a Reference: fast RNA-seq read mapperhomepage
SubreadHigh-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP.homepage
TopHatfast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using Bowtiehomepage
wtdbg2A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.homepage
special purposeBUSCOquantitative measures for the assessment of genome assembly, gene set, and transcriptome completenesshomepage, publication
DEXSeqpackage for finding differential exon usage using RNA-seq exon countspublication, homepage
eXpressstreaming fragment assignment and quantification for high-throughput sequencinghomepage
Geneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
miRDeep2A tool for discovering known and novel miRNAs from small RNA sequencing data.documentation, publication, tutorial
miRExpresstool to analyze high-throughput sequencing data for profiling microRNA expressionhomepage, publication
mirPRoa novel standalone program for differential expression and variation analysis of miRNAshomepage, publication
SortMeRNAa program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic datahomepage
Stackssoftware pipeline for building loci from short-read sequenceshomepage, publication
toolkitFASTXcollection of command line tools for Short-Reads FASTA/FASTQ files preprocessinghomepage
HailHail is an open-source, scalable framework for exploring and analyzing genomic data.homepage
HOMERsuite of tools for Motif Discovery and next generation sequencing analysishomepage
NCBI-TOOLSmore than 700 tools, e.g. for downloading custom data setshomepage
poretoolstoolkit for working with nanopore sequencing data from Oxford Nanoporehomepage
utilitiesBCFtoolsutilities for variant calling and manipulating VCFs and BCFshomepage, tutorial
bcl2fastqdemultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formatshomepage
HTSeqPython package that provides infrastructure to process data from high-throughput sequencing assayspublication, homepage
SRA-Toolkittoolkit to convert .sra files into other formatspublication
variantsBCFtoolsutilities for variant calling and manipulating VCFs and BCFshomepage, tutorial
GATKtoolkit for variant discovery in high-throughput sequencing datahomepage
PilonPilon is an automated genome assembly improvement and variant detection tool.homepage
SNPiRa suite of tools for reliable identification of genomic variants using RNA-seq datapublication
SVDetectSVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data.homepage, manual
visualizationGeneiousa powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualizationhomepage
HailHail is an open-source, scalable framework for exploring and analyzing genomic data.homepage
HiC-ProHiC-Pro: An optimized and flexible pipeline for Hi-C data processing documentation, publication
JMP Genomicsadvanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle)homepage
Loupe Cell BrowserA desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium Single Cell 5' and 3' gene expression data.homepage
ngs.plota standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on NGS data.publication

last modified: 18.07.2019 - 11:48