Bioinformatics Software (listed in alphabetical order)

Name Application purpose Links Program type Module name Server
ABySSNGS, assemblypublication, tutorialcommand line toolABYSSgwdu100, HPC
parallel assembler for short read sequence data
ALLPATHS-LGNGS, assemblyhomepage, tutorialcommand line toolALLPATHSLGgwdu100, HPC
short read genome assembler
AMOSNGS, assemblypublication, tutorialcommand line toolAMOSgwdu100, HPC
modular open source whole genome assembler
AUGUSTUSgene prediction, genomicshomepagecommand line toolAUGUSTUSgwdu100, HPC
gene prediction program for eukaryotes
BamToolsNGS, sequence alignmenttutorialcommand line toolBAMTOOLSgwdu100, HPC
command-line toolkit for for handling genome alignment files
BBMapNGS, sequence alignmenthomepage, tutorialcommand line toolBBMAPgwdu100, HPC
a splice-aware global aligner for DNA and RNA sequencing reads
BCFtoolsNGS, utilities, variantshomepage, tutorialcommand line toolBCFTOOLSgwdu100, HPC
utilities for variant calling and manipulating VCFs and BCFs
bcl2fastqNGS, utilitieshomepagecommand line toolBCL2FASTQgwdu100, HPC
demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats
Beagleanalysis, genomicshomepagecommand line toolBEAGLEgwdu100, HPC
software package for analysis of large-scale genetic data sets
BEASTphylogeneticshomepagecommand line toolBEASTgwdu100, HPC
Software package for phylogenetic analysis with an emphasis on time-scaled trees.
Beast2phylogeneticshomepagecommand line toolBEAST2gwdu100, HPC
Bayesian Evolutionary Analysis by Sampling Trees (rewrite of BEAST)
bedtoolsgenomics, utilitieshomepage, tutorialcommand line toolBEDTOOLSGalaxy, gwdu100, HPC
toolset for genome arithmetic
BESSTNGS, scaffoldingpublication, tutorialcommand line toolBESSTgwdu100, HPC
scaffolding of large fragmented assemblies
BinPackerNGS, assemblypublicationcommand line toolBINPACKERHPC
packing-based de novo transcriptome assembly from RNA-seq data
BioPerltoolkithomepagecommand line toolBIOPERLgwdu100, HPC
open source bioinformatics toolkit for writing bioinformatics scripts
biotoolsutilitieshomepagecommand line toolBIOTOOLSgwdu100, HPC
Python package of bioinformatics utilities
Bowtie 1NGS, sequence alignmenthomepagecommand line toolBOWTIE1Galaxy, gwdu100, HPC
ultrafast, memory-efficient short read aligner
Bowtie 2NGS, sequence alignmenthomepagecommand line toolBOWTIE2Galaxy, gwdu100, HPC
ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
Brackenmetagenomicshomepagecommand line toolBRACKENgwdu100, HPC
A highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses taxonomy labels assigned by Kraken/Kraken2.
BUSCONGS, quality control, special purposehomepage, publicationcommand line toolBUSCOgwdu100, HPC
quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness
BUSTERstructural biologyhomepage, tutorialcommand line toolBUSTERgwdu100, HPC
crystallographic structure refinement using Bayesian statistical methods
Burrows-Wheeler AlignerNGS, sequence alignmenthomepagecommand line toolBWAGalaxy, gwdu100, HPC
software package for mapping low-divergent sequences against a large reference genome
CanuNGS, assembly, nanopore sequencingdocumentationcommand line toolCANUgwdu100, HPC
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
CEASgenomics, special purposehomepagecommand line toolCEASgwdu100, HPC
Cis-regulatory Element Annotation System for characterization of genome-wide protein-DNA interaction patterns from ChIP
Celera AssemblerNGS, assemblyhomepagecommand line toolCELERA_ASSEMBLERgwdu100, HPC
de novo whole-genome shotgun (WGS) DNA sequence assembler
Cell RangerNGS, sequence alignment, single cell analysishomepagecommand line toolCELL_RANGERgwdu100, HPC
A 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.
CiceroNGS, single cell analysishomepagecommand line toolCICEROgwdu100, HPC
Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments.
Circosvisualizationhomepagecommand line toolCIRCOSgwdu100, HPC
software package for visualizing data and information in a circular layout
Clustal Wmultiple sequence alignment, sequence alignmenthomepage, tutorialcommand line toolCLUSTALWgwdu100, HPC
command-line tool for multiple alignment of nucleic acid and protein sequences
Clustal Xmultiple sequence alignment, sequence alignmenthomepage, tutorialgraphical user interfaceCLUSTALXgwdu100, HPC
version of Clustal W with a GUI
CNVnatorgenomics, special purposepublication, tutorialcommand line toolCNVNATORgwdu100, HPC
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
ctffindelectron microscopyhomepagecommand line toolCTFFINDgwdu100, HPC
program for finding CTFs of electron micrographs
CufflinksNGS, analysis, assemblyhomepagecommand line toolCUFFLINKSgwdu100, HPC
assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
CutadaptNGS, filter/trimmingpublication, tutorialcommand line toolCUTADAPTgwdu100, HPC
searches for the adapter in all reads and removes it when found
deepToolsNGS, analysishomepagecommand line toolDEEPTOOLSGalaxy, gwdu100, HPC
command-line tools to process and analyze deep sequencing data
DELLY2analysis, genomics, variantspublication, tutorialcommand line toolDELLY2gwdu100, HPC
structural variant discovery by integrated paired-end and split-read analysis
DESeqNGS, analysispublication, homepagecommand line toolDESEQGalaxy, gwdu100, HPC
differential gene expression of RNA-seq data at the gene level
DETONATENGS, assemblyhomepagecommand line toolDETONATEgwdu100, HPC
de novo transcriptome RNA-seq assembly
DEXSeqNGS, special purposepublication, homepagecommand line toolDEXSEQgwdu100, HPC
package for finding differential exon usage using RNA-seq exon counts
DIALSstructural biologyhomepagecommand line toolDIALSHPC
diffraction integration software for X-ray crystallography
Entrez Directutilitieshomepagecommand line toolEDIRECTgwdu100, HPC
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
EMBOSSanalysis, toolkithomepage, tutorialcommand line toolEMBOSSGalaxy, gwdu100, HPC
analysis package for molecular biology (all programs are listed by command 'wossname', a detailed program description is displayed by 'tfm program_name')
exomePeakNGS, analysispublication, homepagecommand line toolEXOMEPEAKgwdu100, HPC
exome-based analysis for RNA epigenome sequencing data
Exoneratesequence alignmenthomepagecommand line toolEXONERATEgwdu100, HPC
sequence alignment tool for pairwise sequence comparison
eXpressNGS, special purposehomepagecommand line toolEXPRESSgwdu100, HPC
streaming fragment assignment and quantification for high-throughput sequencing
FASTAsequence alignmenthomepagecommand line toolFASTAgwdu100, HPC
sequence comparison
FastQCNGS, quality controlhomepagecommand line toolFASTQCGalaxy, gwdu100, HPC
quality control tool for high throughput sequence data
fastStructureNGS, phylogeneticshomepage, publicationcommand line toolFASTSTRUCTUREgwdu100, HPC
A variational framework for inferring population structure from SNP genotype data.
FASTXNGS, toolkithomepagecommand line toolFASTXgwdu100, HPC
collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
FiltlongNGS, filter/trimminghomepagecommand line toolFILTLONGgwdu100, HPC
Filtlong is a tool for filtering long reads by quality.
FitHiChIPHi-C, NGShomepage, publicationcommand line toolFITHICHIPgwdu100, HPC
Statistically Significant loops from HiChIP data
FlappieNGS, nanopore sequencinghomepagecommand line toolFLAPPIEgwdu100, HPC
Flip-flop basecaller for Oxford Nanopore reads.
FlyeNGS, assembly, nanopore sequencinghomepagecommand line toolFLYEgwdu100, HPC
Flye is a de novo assembler for single molecule sequencing reads.
freebayesSNP, variantshomepagecommand line toolFREEBAYESgwdu100, HPC
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
GapFillerNGS, scaffoldingpublicationcommand line toolGAPFILLERgwdu100, HPC
stand-alone program for closing gaps within pre-assembled scaffolds
GATKNGS, variantshomepagecommand line toolGATKgwdu100, HPC
toolkit for variant discovery in high-throughput sequencing data
GeneiousNGS, analysis, assembly, molecular biology, sequence alignment, special purpose, visualizationhomepagegraphical user interfaceGENEIOUSgwdu100
a powerful and comprehensive suite of molecular biology and NGS analysis tools with very good visualization
GenomeToolsanalysis, genomicshomepagecommand line toolGENOMETOOLSgwdu100, HPC
bioinformatics tools for genome analysis
GMAP/GSNAPsequence alignmenthomepagecommand line toolGMAPgwdu100, HPC
GMAP: Genomic Mapping and Alignment Program for mRNA and EST Sequences. GSNAP: Genomic Short-read Nucleotide Alignment Program
Gromacsstructural biologyhomepagecommand line toolGROMACSHPC
a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles
GuppyNGS, nanopore sequencinghomepagecommand line toolGUPPYgwdu100, HPC
Accelerated basecaller for Oxford Nanopore Sequencing
HailNGS, analysis, annotation, quality control, toolkit, visualizationhomepagecommand line toolHAILHPC
Hail is an open-source, scalable framework for exploring and analyzing genomic data.
HMMERsequence alignment, special purposehomepagecommand line toolHMMERgwdu100, HPC
biosequence analysis using profile hidden Markov models
HiC-ProHi-C, NGS, visualizationdocumentation, publicationcommand line toolHIC-PROgwdu100, HPC
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
hichipperHi-C, NGS, quality controlhomepage, documentationcommand line toolHICHIPPERgwdu100, HPC
hichipper is a command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data.
HISAT2NGS, sequence alignmenthomepagecommand line toolHISAT2Galaxy, gwdu100, HPC
A fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
HOMERNGS, analysis, toolkithomepagecommand line toolHOMERgwdu100, HPC
suite of tools for Motif Discovery and next generation sequencing analysis
HTSeqNGS, utilitiespublication, homepagecommand line toolHTSEQGalaxy, gwdu100, HPC
Python package that provides infrastructure to process data from high-throughput sequencing assays
IDBANGS, assemblyhomepagecommand line toolIDBAgwdu100, HPC
de novo assembler for short reads sequencing data with highly uneven sequencing depths
Integrative Genomics Viewergenome browser, genomics, visualizationhomepage, publicationgraphical user interfaceIGVgwdu100, HPC
high-performance visualization tool for genomic datasets
iMOSFLMstructural biologyhomepagegraphical user interfaceiMOSFLMHPC
a program for integrating single crystal diffraction data from area detectors
InterProScananalysis, protein, special purposehomepage, publicationcommand line toolINTERPROSCANgwdu100, HPC
protein sequence search
ipyradNGS, RADseq, analysis, assemblydocumentationcommand line toolIPYRADgwdu100, HPC
interactive assembly and analysis of RADseq data sets
Jellyfishutilitieshomepage, tutorialcommand line toolJELLYFISHgwdu100, HPC
A tool for fast, memory-efficient counting of k-mers in DNA
JMP GenomicsNGS, genomics, visualizationhomepagegraphical user interfaceGWD-WinTSBio
advanced genomic data analysis software with very good visualization (part of the SAS-JMP-bundle)
kallistoNGS, analysishomepage, publicationcommand line toolKALLISTOgwdu100, HPC
program for quantifying abundances of transcripts from RNA-Seq data
KatualiNGS, analysis, nanopore sequencinghomepage, documentationcommand line toolKATUALIgwdu100, HPC
Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data.
KisSpliceNGS, assemblyhomepagecommand line toolKISSPLICEgwdu100, HPC
local transcriptome assembler for SNPs, indels and AS events
KNIMEutilitieshomepagegraphical user interfaceKNIMEgwdu100
more than 1500 modules, hundreds of ready-to-run examples, community contributions, and tool integrations
Kraken2classification, metagenomicshomepagecommand line toolKRAKEN2gwdu100, HPC
A taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. The assisting tool Bracken is available in a separate module.
kSNPSNP, phylogenetics, variantshomepagecommand line toolKSNPgwdu100, HPC
kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.
LoRDECNGS, quality controlhomepagecommand line toolLORDECgwdu100, HPC
LoRDEC 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.
Loupe Cell BrowserNGS, analysis, visualizationhomepagegraphical user interfaceGWD-WinTSBio
A 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.
MACS2ChIP-Seq, NGS, analysishomepagecommand line toolMACS2Galaxy, gwdu100, HPC
Model-based Analysis of ChIP-Seq data for identifying transcript factor binding sites
MAFFTmultiple sequence alignment, sequence alignmenthomepage, publicationcommand line toolMAFFTgwdu100, HPC
multiple alignment program for amino acid or nucleotide sequences
MAKERannotation, genomicshomepage, publicationcommand line toolMAKERgwdu100, HPC
genome annotation pipeline
MarkerMinerNGS, analysis, phylogeneticshomepage, publicationcommand line toolMARKERMINERgwdu100, HPC
fully automated workflow and application for discovery of SCN loci in angiosperms
MARVELNGS, assembly, nanopore sequencinghomepagecommand line toolMARVELgwdu100, HPC
MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.
Mauvemultiple sequence alignment, sequence alignmenthomepage, publicationgraphical user interfaceMAUVEGalaxy, gwdu100, HPC
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
MedakaNGS, nanopore sequencinghomepage, documentationcommand line toolMEDAKAgwdu100, HPC
Medaka is a tool to create a consensus sequence from nanopore sequencing data.
MEMEanalysis, special purpose, toolkithomepagecommand line toolMEMEGalaxy, gwdu100, HPC
supports motif-based analysis of DNA, RNA and protein sequences
MiniasmNGS, assembly, nanopore sequencinghomepagecommand line toolMINIASMgwdu100, HPC
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Minimap2NGS, nanopore sequencing, sequence alignmenthomepage, publication, manualcommand line toolMINIMAP2gwdu100, HPC
A versatile pairwise aligner for genomic and spliced nucleotide sequences
MIRANGS, assemblyhomepagecommand line toolMIRAgwdu100, HPC
a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNA-seq projects
miRDeep2NGS, analysis, special purposedocumentation, publication, tutorialcommand line toolMIRDEEP2gwdu100, HPC
A tool for discovering known and novel miRNAs from small RNA sequencing data.
miRExpressNGS, analysis, special purposehomepage, publicationcommand line toolMIREXPRESSgwdu100, HPC
tool to analyze high-throughput sequencing data for profiling microRNA expression
Miropeatsvisualizationhomepagecommand line toolMIROPEATSgwdu100, HPC
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and presents this similarity information graphically.
mirPRoNGS, analysis, special purposehomepage, publicationcommand line toolMIRPROgwdu100, HPC
a novel standalone program for differential expression and variation analysis of miRNAs
Monocle3single cell analysishomepagecommand line toolMONOCLE3gwdu100, HPC
Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.
mothurmicrobial ecologyhomepagecommand line toolMOTHURgwdu100, HPC
open-source expandable software for the bioinformatic needs of microbial ecology
MOTHUR-GUImicrobial ecologyhomepagegraphical user interfaceMOTHUR-GUIgwdu100, HPC
Gui version of mothur
MrBayesphylogeneticshomepagecommand line toolMRBAYESgwdu100, HPC
program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
MUMmersequence alignmenthomepagecommand line toolMUMMERgwdu100, HPC
a system for rapidly aligning entire genomes
MUSCLEmultiple sequence alignmenthomepage, publicationcommand line toolMUSCLEgwdu100, HPC
multiple sequence alignment
NanofiltNGS, filter/trimming, nanopore sequencinghomepage, publicationcommand line toolNANOFILTgwdu100, HPC
Filtering and trimming of long read sequencing data
NanopolishNGS, assembly, nanopore sequencingmanualcommand line toolNANOPOLISHgwdu100, HPC
Software package for signal-level analysis of Oxford Nanopore sequencing data
NanoStatNGS, nanopore sequencinghomepage, publicationcommand line toolNANOSTATgwdu100, HPC
Create statistic summary of an Oxford Nanopore read dataset
NCBI-BLASTclassification, sequence alignmenthomepagecommand line toolNCBI-BLASTGalaxy, gwdu100, HPC
basic local alignment search tool
NCBI-TOOLSNGS, toolkithomepagecommand line toolNCBI-TOOLSgwdu100, HPC
more than 700 tools, e.g. for downloading custom data sets
ngs.plotNGS, visualizationpublicationcommand line toolNGSPLOTgwdu100, HPC
a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on NGS data.
OasesNGS, assemblyhomepage, publicationcommand line toolOASESgwdu100, HPC
de novo transciptome assembler for very short reads
PartitionFinderphylogeneticshomepagecommand line toolPARTITIONFINDERgwdu100, HPC
select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses
PauvreNGS, genome browser, nanopore sequencinghomepagecommand line toolPAUVREHPC
QC and genome browser plotting Oxford Nanopore and PacBio long reads
PGURE-SVTmicroscopyhomepage, publicationcommand line toolPGURESVTgwdu100, HPC
algorithm for denoising time-resolved microscopy image sequences
phASERspecial purposehomepage, publicationcommand line toolPHASERgwdu100, HPC
phasing and Allele Specific Expression from RNA-seq
PHYLIPphylogeneticshomepagecommand line toolPHYLIPgwdu100, HPC
PHYLogeny Inference Package: programs for inferring phylogenies
PhyMLphylogeneticshomepagecommand line toolPHYMLGalaxy, gwdu100, HPC
Phylogenetic estimation using (Maximum) Likelihood
PicardNGShomepagecommand line toolPICARDGalaxy, gwdu100, HPC
set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF
PilonNGS, assembly, variantshomepagecommand line toolPILONgwdu100, HPC
Pilon is an automated genome assembly improvement and variant detection tool.
PlatanusNGS, assemblyhomepage, publicationcommand line toolPLATANUSgwdu100, HPC
PLATform 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 data
PLINKanalysis, genomics, toolkithomepagecommand line toolPLINKgwdu100, HPC
whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
POPBAMNGS, phylogeneticspublicationcommand line toolPOPBAMgwdu100, HPC
tools for evolutionary analysis of short read sequence alignments
PomoxisNGS, analysis, nanopore sequencingdocumentationcommand line toolPOMOXISgwdu100, HPC
Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.
PorechopNGS, filter/trimming, nanopore sequencinghomepagecommand line toolPORECHOPHPC
adapter trimmer for Oxford Nanopore reads
poretoolsNGS, nanopore sequencing, toolkithomepagecommand line toolPORETOOLSgwdu100, HPC
toolkit for working with nanopore sequencing data from Oxford Nanopore
PROFphdprotein, structural biologyhomepagecommand line toolPROFPHDgwdu100, HPC
Predicts protein secondary structure using a system of neural networks
Proteome Discovererproteinhomepagegraphical user interfaceGWD-WinTSBio
only usable as viewer on our server
pyRADNGS, RADseq, assembly, phylogeneticspublicationcommand line toolPYRADgwdu100, HPC
assembly of de novo RADseq loci for phylogenetic analyses
QUASTNGS, quality controlhomepage, manualcommand line toolQUASTgwdu100, HPC
QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
RaconNGS, assemblypublication, tutorialcommand line toolRACONgwdu100, HPC
ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
RAxMLphylogeneticshomepagecommand line toolRAXMLgwdu100, HPC
Randomized Axelerated Maximum Likelihood: tool for maximum-likelihood based phylogenetic inference
RAxML Next Generationphylogeneticsdocumentation, publicationcommand line toolRAXML-NGgwdu100, HPC
A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
RECONgenomics, special purposehomepage, publicationcommand line toolRECONgwdu100, HPC
program for prediction of nucleosome formation potential
RELIONelectron microscopytutorialgraphical user interfaceRELIONgwdu100, HPC
REgularised LIkelihood OptimisatioN: a program for an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy
RepeatMaskergenomics, special purposehomepagecommand line toolREPEATMASKERgwdu100, HPC
program that screens DNA sequences for interspersed repeats and low complexity DNA sequences
Rguistatisticshomepagegraphical user interfaceGWD-WinTSBio
graphical user interface for R
Rosettaprotein, structural biologyhomepagecommand line toolROSETTAHPC
software suite including algorithms for computational modeling and analysis of protein structures
RSEMNGS, analysispublicationcommand line toolRSEMgwdu100, HPC
accurate transcript quantification from RNA-Seq data with or without a reference genome
RSeQCNGS, quality controlhomepagecommand line toolRSEQCgwdu100, HPC
a package that provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data
Rstudiostatisticshomepagegraphical user interfaceGWD-WinTSBio
A free and open-source environment for R, a programming language for statistical computing. Also available as RStudio-Server.
SalmonNGS, analysishomepagecommand line toolSALMONgwdu100, HPC
A tool for quantifying the expression of transcripts using RNA-seq data.
SamtoolsNGS, sequence alignment, utilitieshomepagecommand line toolSAMTOOLSGalaxy, gwdu100, HPC
various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
ScallopNGS, assemblyhomepage, publicationcommand line toolSCALLOPHPC
Scallop is a reference-based transcriptome assembler for RNA-seq.
ScrappieNGS, nanopore sequencinghomepagecommand line toolSCRAPPIEHPC
Basecaller for Oxford Nanopore Sequencing
ShastaNGS, nanopore sequencingdocumentationcommand line toolSHASTAgwdu100, HPC
De novo assembly from Oxford Nanopore reads.
SignalPprotein, special purposehomepage, publicationcommand line toolSIGNALPgwdu100, HPC
prediction of presence and location of signal peptide cleavage sites in amino acid sequences
simRRLsphylogenetics, special purposehomepagecommand line toolSIMRRLSgwdu100, HPC
simulation of raw restriction-site associated DNA fastq files for testing assembly methods on raw data
SINAmultiple sequence alignment, sequence alignmenthomepage, publicationcommand line toolSINAgwdu100, HPC
tool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracy
SMARTdenovoNGS, assembly, nanopore sequencinghomepagecommand line toolSMARTDENOVOgwdu100, HPC
Ultra-fast de novo assembler using long noisy reads.
SNAPgene prediction, genomicshomepagecommand line toolSNAPgwdu100, HPC
Semi-HMM-based Nucleic Acid Parser: a gene prediction tool
SnippyNGS, SNP, variantshomepagecommand line toolSNIPPYgwdu100, HPC
Rapid haploid variant calling and core genome alignment
SnpEffannotation, variantshomepagecommand line toolSNPEFFGalaxy, gwdu100, HPC
Genomic variant annotations and functional effect prediction toolbox.
SNPiRNGS, SNP, analysis, variantspublicationcommand line toolSNPIR-TOOLgwdu100, HPC
a suite of tools for reliable identification of genomic variants using RNA-seq data
SOAPalignerNGS, sequence alignmenthomepagecommand line toolSOAP2-ALIGNERgwdu100, HPC
alignment tool
SOAPdenovoNGS, assemblyhomepagecommand line toolSOAP2-DENOVOgwdu100, HPC
de novo short reads assembler
SOAPdenovo-TransNGS, assemblyhomepage, publicationcommand line toolSOAP-DENOVO-TRANSgwdu100, HPC
A de novo transcriptome assembler designed specifically for RNA-Seq.
SortMeRNANGS, filter/trimming, special purposehomepagecommand line toolSORTMERNAgwdu100, HPC
a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data
SPAdesNGS, assemblyhomepage, manualcommand line toolSPADESgwdu100, HPC
An assembly toolkit containing various assembly pipelines.
SRA-ToolkitNGS, utilitiespublicationcommand line toolSRATOOLKITGalaxy, gwdu100, HPC
toolkit to convert .sra files into other formats
SRST2special purposehomepagecommand line toolSRST2gwdu100, HPC
Short Read Sequence Typing for Bacterial Pathogens
SSPACE-LongReadNGS, scaffoldinghomepage, publicationcommand line toolSSPACE-LONGREADgwdu100, HPC
a program for scaffolding longreads (e.g. PacBio RS reads)
SSPACE-StandardNGS, scaffoldinghomepage, publicationcommand line toolSSPACE-STANDARDgwdu100, HPC
a program for scaffolding pre-assembled contigs using NGS paired-read data
StacksNGS, special purposehomepage, publicationcommand line toolSTACKSgwdu100, HPC
software pipeline for building loci from short-read sequences
Staden PackageNGS, analysis, assemblyhomepagegraphical user interfaceSTADENgwdu100, HPC
tools for DNA sequence assembly, editing and sequence analysis
STARNGS, sequence alignmenthomepagegraphical user interfaceSTARGalaxy, gwdu100, HPC
Spliced Transcript Alignment to a Reference: fast RNA-seq read mapper
Structurephylogeneticshomepagegraphical user interfaceSTRUCTUREgwdu100, HPC
A software package for using multi-locus genotype data to investigate population structure.
SubreadNGS, SNP, counting, sequence alignmenthomepagecommand line toolSUBREADGalaxy, gwdu100, HPC
High-performance read alignment, quantification and mutation discovery. The package contains the programs Subread, Subjunc, featureCounts, Sublong and exactSNP.
SVDetectNGS, variantshomepage, manualcommand line toolSVDETECTgwdu100, HPC
SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data.
Tabixgenomics, special purposehomepage, publicationcommand line toolTABIXgwdu100, HPC
tool for fast retrieval of sequence features from generic TAB-delimited files
Tandem Repeats Findergenomics, special purposehomepagecommand line toolTANDEMREPEATSFINDERgwdu100, HPC
a program to locate and display tandem repeats in DNA sequences
T-Coffeemultiple sequence alignment, sequence alignmenthomepagecommand line toolTCOFFEEgwdu100, HPC
a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods
Tomahawkspecial purposehomepagecommand line toolTOMAHAWKgwdu100, HPC
Fast calculations of linkage-disequilibrium in large-scale human cohorts
TopHatNGS, sequence alignmenthomepagecommand line toolTOPHATGalaxy, gwdu100, HPC
fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using Bowtie
Trans-ABySSNGS, assemblyhomepage, publicationcommand line toolTRANSABYSSHPC
de novo assemly of RNA-Seq data
TransrateNGS, assembly, quality controlhomepagecommand line toolTRANSRATEgwdu100
software for de-novo transcriptome assembly quality analysis
Trim Galore!NGS, filter/trimming, quality controlhomepagecommand line toolTRIMGALOREgwdu100, HPC
wrapper tool around Cutadapt and FastGC to consistently apply quality and adapter trimming to FastQ files
TrimmomaticNGS, filter/trimminghomepagecommand line toolTRIMMOMATICGalaxy, gwdu100, HPC
flexible trimmer for Illumina NGS data
TRINITYNGS, assemblyhomepage, publicationcommand line toolTRINITYGalaxy, gwdu100, HPC
de novo reconstruction of transcriptomes from RNA-Seq data
tRNAscan_SEgenomics, special purposehomepage, publicationcommand line toolTRNASCAN-SEgwdu100, HPC
a program for improved detection of transfer RNA genes in genomic sequence
UCSCgenome browser, genomicshomepagecommand line toolUCSCgwdu100, HPC
genome browser
VelvetNGS, assemblyhomepagecommand line toolVELVETgwdu100, HPC
sequence assembler for very short reads
VEPSNP, variantshomepagecommand line toolVEPgwdu100, HPC
Variant Effect Predictor predicts the functional effects of genomic variants.
Vienna RNA packagestructural biologyhomepagecommand line toolVIENNA-RNAgwdu100, HPC
C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures
Vlionelectron microscopyhomepage, tutorialgraphical user interfaceVLIONHPC
A slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code.
wtdbg2NGS, assembly, nanopore sequencing, sequence alignmenthomepagecommand line toolWTDBG2gwdu100, HPC
A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.

last modified: 14.05.2020 - 11:04