Software supported by NCGAS
The National Center for Genome Analysis Support (NCGAS) and its collaborators maintain the following genome analysis packages on Carbonate at Indiana University, on Bridges at Pittsburgh Supercomputing Center (PSC), and via images on Jetstream2. For more information on a package, click its name. If the package you need is not listed in the table below, contact the UITS Research Applications and Deep Learning team.
Package | Description | Version | Carbonate | Bridges | Jetstream2 |
---|---|---|---|---|---|
abyss | Parallel assembler for short read sequence data |
1.5.2 | ✔Yes | ✔Yes | Genomics Toolkit |
1.9.0 | ✔Yes | ||||
2.0.2 | ✔Yes | ✔Yes | |||
AllPaths-LG | Whole-genome shotgun assembler using Illumina long and short read library |
524888 | ✔Yes | ||
Annovar | Functionally annotates genetic variants detected from diverse genomes |
2016.02.01 | ✔Yes | ||
AFNI | Processing, analyzing, and displaying functional MRI (FMRI) data |
22.0.04 | ✔Yes | ||
Anvi'o | Analysis and visualization of genomics data |
2.0.2 | ✔Yes | ||
2.2.2 | ✔Yes | ||||
2.3.1 | ✔Yes | ||||
2.3.2 | ✔Yes | ||||
2.4.0 | ✔Yes | ||||
3.0.0 | ✔Yes | ||||
ARAGORN | Detects tRNA, mtRNA and tmRNA genes |
1.2.3 | ✔Yes | ||
augustus | Predicts genes in eukaryotic genomic sequences |
3.3 | ✔Yes | Genome assembly workshop | |
3.2 | ✔Yes | ||||
autodocksuite | Predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure |
4.2.6 | ✔Yes | ||
bamtools | C++ API and toolkit for analyzing and managing BAM files |
2.4.0 | ✔Yes | ||
2.4.1 | ✔Yes | ||||
bamutil | Several programs that perform operations on SAM/BAM files |
1.0.13 | bcbio-nextgen toolkit v.2.0 | ||
1.0.14 | ✔Yes | ||||
Barrnap | Predicts location of ribosomal RNA genes in genomes |
0.6 | ✔Yes | ||
bbmap | Short read aligner for DNA and RNA-seq data |
38.6 | Genomics Toolkit | ||
bcftools | Discovery of correlated genomic features, such as ESTs, polymorphisms, and mobile elements |
1.3.1 | ✔Yes | Genomics Toolkit | |
0.1.19 | ✔Yes | ||||
1.5 | ✔Yes | ||||
Bedops | Scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale |
2.4.19 | ✔Yes | ||
2.4.35 | ✔Yes | ||||
BLASR | Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement |
1.3.1 | ✔Yes | ✔Yes | |
bedtools | Discovery of correlated genomic features, such as ESTs, polymorphisms, and mobile elements |
2.20.1 | |||
2.26.0 | ✔Yes | ||||
2.25.0 | ✔Yes | ||||
bioconductor | R packages for analysis and comprehension of high-throughput genomic sequence data |
2.12 | |||
3.3 | ✔Yes | ||||
3.6 | ✔Yes | ||||
3.9 | ✔Yes | ||||
biopython | Collection of Python packages to support bioinformatics |
1.59 | bcbio-nextgen toolkit v.2.0 | ||
1.7.0 | ✔Yes | ||||
1.7.3 | ✔Yes | ||||
Bismark | Program to map bisulfite treated sequencing reads to a genome of interest |
0.19.0 | ✔Yes | ✔Yes | |
blast | Search tool that finds regions of local similarity between nucleotide or protein sequences |
2.6.0+ | ✔Yes | ✔Yes | |
2.2.31 | ✔Yes | ||||
2.7.1 | ✔Yes | ||||
blat | Alignment tool like BLAST, but structured differently |
35 | ✔Yes | ✔Yes | |
bowtie | Ultrafast, memory-efficient short read aligner. See related tool Bowtie2. |
1.1.2 | ✔Yes | ||
1.1.1 | ✔Yes | ||||
1.2.2 | ✔Yes | ||||
bowtie2 | Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie. |
2.1.0 | |||
2.2.7 | ✔Yes | ||||
2.3.2 | ✔Yes | ||||
2.3.4.1 | ✔Yes | ||||
busco | Assesses genome assembly and annotation completeness |
3.0.2 | ✔Yes | ||
1.22 | ✔Yes | ||||
breseq | Finds mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes |
0.30.2 | ✔Yes | ||
0.32.0 | ✔Yes | ||||
bwa | Fast light-weight tool that aligns relatively short sequences to a sequence database |
0.6.2 | |||
0.7.12 | ✔Yes | ||||
cafe | Analyze changes in gene family size for evolutionary inferences |
4.2 | ✔Yes | ||
canu | Fork of the Celera Assembler designed for high-noise single-molecule sequencing |
1.3 | ✔Yes | ||
1.5 | ✔Yes | ||||
1.6 | ✔Yes | ✔Yes | |||
1 | ✔Yes | ||||
cd-hit | Tool to cluster and compare protein or nucleotide sequences |
4.6. | ✔Yes | ||
2016.06.21 | ✔Yes | ||||
centrifuge | Rapid and efficient classification of DNA sequences from microbial samples |
1.0.3 | ✔Yes | ✔Yes | |
1.0.4 | ✔Yes | ||||
cfsan | Python based SNP pipelines | 1.0.1 | ✔Yes | ||
checkm | Tools for assessing genome quality recovered from isolates, single cells or metagenomes |
1.0.7 | ✔Yes | Arkansas Workshop | |
Circos | Produces visualizations in a circular layout, commonly used for genomics data |
0.69.2 | ✔Yes | ||
clustalw2 | Multiple alignment of nucleic acid and protein sequences |
2.1 | ✔Yes | ||
crisprdo | Evaluate the goodness of an sgRNA in both sensitivity and specificity |
1 | bcbio-nextgen toolkit v.2.0 | ||
cufflinks | Assembles transcripts, estimates their abundances, tests for differential expression and regulation in RNA-Seq samples |
2.0.2 | Genomics Toolkit | ||
2.2.1 | ✔Yes | ✔Yes | |||
cutadapt | Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output |
1.11 | Genomics Toolkit | ||
1.16 | ✔Yes | ✔Yes | |||
1.1 | ✔Yes | ||||
1.5 | ✔Yes | ||||
1.9.1 | ✔Yes | ||||
cytoscape | Platform for visualizing complex-networks and integrating these with attribute data |
3.6.1 | ✔Yes | ||
Dammit | Simple de novo transcriptome annotator |
0.3 | ✔Yes | ||
deepTools | Suite of Python tools for the efficient analysis of high-throughput sequencing data |
2.3.5 | ✔Yes | ||
3.1.3 | ✔Yes | ||||
Detonate | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation |
1.1 | ✔Yes | ||
Diamond | Alignment tool for aligning short DNA sequencing reads to a protein reference database |
0.7.11 | ✔Yes | ||
0.8.31 | ✔Yes | ||||
0.8.3 | ✔Yes | ||||
0.9.13 | ✔Yes | ||||
Dimspy | Processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data |
1.03 | ✔Yes | ||
Discovar | Variant caller and small genome assembler |
52488 | ✔Yes | ||
Discovar de novo | Large (and small) de novo genome assembler |
52488 | ✔Yes | ||
discasm | Extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads |
0.1.2 | ✔Yes | ||
Drupal7 | Drupal provides a back-end framework for at least 2.3% of all websites worldwide |
||||
ECTools | Long read correction, plus other correction tools |
12/1/2014 | ✔Yes | ||
E-utilities | Table interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI) |
6/24/2015 | Mining SRA to identify datasets | ||
EPA-ng | Perform maximum likelihood-based phylogenetic placement of genetic sequences |
0.1.0-beta | ✔Yes | ||
edge-pro | EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. |
Genomics Toolkit | |||
emboss | A high-quality package of free, Open Source software for molecular biology |
6.6.0 | ✔Yes | ||
EricScript | Computational framework for the discovery of gene fusions in paired end RNA-seq data. |
0.5.5 | ✔Yes | ||
ensembl | Various tools to assist in use and analysis of Ensembl data |
95.1 | ✔Yes | ||
evigene | Pipeline script for processing large piles of transcript assemblies, from several methods into the most biologically useful set of mRNA, classified into primary and alternate transcripts |
2013.07.27 | ✔Yes | ||
exonerate | Exonerate is a general purpose tool for biological sequence comparison |
2.4 | ✔Yes | ✔Yes | |
Falcon | Collection of genome assembly tools |
0.4.1 | ✔Yes | ||
fasta3 | The FASTA package - protein and DNA sequence similarity searching and alignment programs |
Genomics Toolkit | |||
fastqc | Quality control for high-throughput sequence data |
0.10.1 | |||
0.11.3 | ✔Yes | ||||
0.11.5 | ✔Yes | ||||
FASTA-Splitter | Divides a single FASTA file into multiple files |
0.2.4 | ✔Yes | ||
0.1.2 | ✔Yes | ||||
fastx | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing |
0.0.14 | ✔Yes | ||
flash | Fast and accurate tool to merge paired-end reads from NGS experiments |
1.2.11 | ✔Yes | ||
FragGeneScan | Finds fragmented genes in short reads and predicts prokaryotic genes in incomplete assemblies or complete genomes |
1.2 | ✔Yes | ||
Freebayes | Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs and complex events |
1.2.0 | ✔Yes | ||
gatk | Genome Analysis Toolkit, for high-throughput sequencing data |
3 | ✔Yes | ||
3.5 | ✔Yes | ||||
3.6 | ✔Yes | ||||
3.7 | ✔Yes | ||||
4.0.1.2 | ✔Yes | ||||
4.beta.5 | ✔Yes | ||||
Genome MuSiC | Tools to discover the significance of somatic mutations found in a cohort of cancer samples, and with respect to various external data sources |
0.4.1 | ✔Yes | ||
GFFRead | GFF/GTF parsing utility providing format conversions, region filtering, and FASTA sequence extraction |
0.9.8 c | ✔Yes | ||
Glimmer | Gene Locator and Interpolated Markov ModelER to identify coding regions |
3.0.2 | ✔Yes | ||
3.0.4 | ✔Yes | ||||
GraPhlan | Tool for producing high quality circular representations of taxonomic and phylogenetic trees |
0.9.7 | ✔Yes | ||
gmap | Align cDNA to reference to determine gene structure and structural variants |
2017-06-20 | ✔Yes | ||
2018-05-11 | ✔Yes | ||||
gmapfusion | Identifying candidate fusion transcripts based on transcript sequences |
0.3.0 | ✔Yes | ||
guppy | Oxford Nanopore Technologies' basecalling algorithms |
3.1.5-cpu | ✔Yes | ||
hisat2 | Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome |
0.1.6-beta | |||
2.0.4 | ✔Yes | ||||
2.1.0 | ✔Yes | ||||
hmmer | Biosequence analysis using profile hidden Markov models |
3 | Genome assembly workshop | ||
3.1.b2 | ✔Yes | ✔Yes | |||
HUMAnN2 | Pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomatic sequencing data |
0.10.0 | ✔Yes | ||
htseq | Analysis of high-throughput sequencing data using Python |
0.9.1 | ✔Yes | ✔Yes | bcbio-nextgen toolkit v.2.0 |
htslib | C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data |
1.5 | ✔Yes | ||
IDBA | Iterative De Bruijn Graph De Novo Assembler short read assembler for transcriptomes |
1.1.1 | ✔Yes | ||
IGV | The Integrative Genomics Viewer (IGV) is a high-performance visualization tool |
Genomics Toolkit | |||
ipython/Jupyter | Interactive Python shell | ✔Yes | bcbio-nextgen toolkit v.2.0 | ||
Ipyrad | Interactive toolkit for assembly and analysis of restriction-site associated genomic data sets â€" RAD, RADseq, GBS |
0.7.2 | ✔Yes | ||
Interproscan | Overview of the families that a protein belongs to and the domains sites in the sequences |
5.29-6 | ✔Yes | ||
Jellyfish/Jellyfish2 | Tool for fast, memory efficient counting of k-mers in DNA |
1.1.11 | ✔Yes | bcbio-nextgen toolkit v.2.0, | |
2.2.6 | ✔Yes | ||||
2.2.9 | ✔Yes | ||||
Jbrowse | JBrowse is a fast, scalable genome browser built completely with JavaScript and HTML5. |
||||
kallisto | Quantifies abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads |
0.43.0 | ✔Yes | ||
0.43.1 | ✔Yes | ||||
khmer | Tools to work with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells |
2.0.0 | ✔Yes | ||
2.1.1 | ✔Yes | ||||
Kraken | System for assigning taxonomic labels to short DNA sequences |
0.10.5 | ✔Yes | bcbio-nextgen toolkit v.2.0 | |
1 | ✔Yes | ||||
2.0.7 | ✔Yes | ||||
Longranger | Analysis pipelines that processes Chromium sequencing (10X) output |
2.1.6 | ✔Yes | Genome assembly workshop | |
Loupe | Loupe Cell Browser gene expression tutoria |
Genome assembly workshop | |||
macs | Model-based Analysis of ChIP-Seq, for identifying transcript factor binding sites |
1.4.2 | bcbio-nextgen toolkit v.2.0 | ||
1.4.3 | ✔Yes | ||||
2.1.0 | ✔Yes | ||||
2.1.2 | ✔Yes | ||||
MACSE | Aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons |
1.2 | ✔Yes | ||
MAFFT | Multiple sequence alignment program |
7.3 | ✔Yes | ||
manta | Structural variant and indel caller for mapped sequencing data |
1.4.0 | Genomics Toolkit | ||
maker | Ab initio gene predictions | 2.31.10 | ✔Yes | ||
2.31.9 | ✔Yes | ||||
mash | MinHash dimensionality-reduction technique for clustering abd searching massive sequence collections |
2.1.1 | ✔Yes | ||
masurca | Assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches. |
3.2.0 | ✔Yes | ||
3.1.3 | ✔Yes | ||||
3.2.2 | ✔Yes | ||||
3.2.6 | ✔Yes | ||||
3.2.7 | ✔Yes | ||||
mcl | Scalable unsupervised clustering algorithm |
14-137 | ✔Yes | ||
megahit | A single node assembler for large and complex metagenomics NGS reads, such as soil |
1.1.2 | ✔Yes | Arkansas Workshop | |
1.1.1 | ✔Yes | ||||
MALT | MEGAN Alignment Tool, and extension of MEGAN |
0.3.8 | ✔Yes | ||
Mapsembler 2 | Targeted assembly software | 2.2.4 | ✔Yes | ||
MaxBin | Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm |
2.1.1 | ✔Yes | ||
MEGAN | MEta Genome ANalyzer | 5.11.3 | ✔Yes | MEGAN community edition | |
6 | ✔Yes | ||||
metabat | Metagenome binning tool | 2.11.3 | ✔Yes | Arkansas Workshop | |
Meraculous | Whole genome assembler for Next Generation Sequencing data geared for large genomes |
2.2.4 | ✔Yes | ||
MetaPhlAn | Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data |
1.7.7 | ✔Yes | ||
2.6.0 | ✔Yes | ||||
MetaVelvet | Extension of Velvet assembler to de novo metagenome assembly from short sequence reads |
1.2.10 | ✔Yes | ||
Metapalette | k-mer based bacterial community reconstruction technique |
1 | ✔Yes | ||
MinCED | Program to find CRISPRs in full genomes or environmental datasets such as metagenomes |
0.2.0 | ✔Yes | ||
minia | Minia is a short-read assembler based on a de Bruijn graph |
2.0.7 | ✔Yes | ||
mira | Assembler | 4.0.2 | ✔Yes | ||
mothur | Bioinformatics tool for analyzing 16S rRNA gene sequences |
1.38.1 | ✔Yes | ||
1.40.5 | ✔Yes | ||||
1.41.3 | ✔Yes | ||||
mrbayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models |
3.2.1 mpi | Genomics Toolkit | ||
MUctect | Identification of somatic point mutations in next generation sequencing data of cancer genomes. |
bcbio-nextgen toolkit v.2.0 | |||
MultiQC | Aggregate results from bioinformatics analyses across many samples into a single report |
Genomics toolkit | |||
mummer | System for rapidly aligning entire genomes, whether in complete or draft form |
3.23 | ✔Yes | ✔Yes | |
muscle | MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests |
3.8.31 | ✔Yes | ✔Yes | |
MyCC | Automated binning tool that visualizes metagenomes and identifies reconstructed genomic fragments |
42341 | ✔Yes | ||
nanopack | Long read processing and analysis |
0.1.14 | ✔Yes | ||
Nasp | Pipleine to identify SNP's in the data. |
1.1.2 | ✔Yes | ||
NGSCheckMate | Identifies NGS data files from the same individual |
2016.10.12 | ✔Yes | ||
novoalign | Aligns short reads to reference genome for resequencing experiments |
3. .0 | ✔Yes | bcbio-nextgen toolkit v.2.0 | |
oases | De novo transcriptome assembler for very short reads |
0.2.09 | ✔Yes | ||
OpenRefine | Open source, power tool for working with messy data. |
EML Workshop (private image) | |||
paml | Phylogenetic analyses of DNA or protein sequences using maximum likelihood |
4.9 | ✔Yes | ||
paup | Phylogenetic Analysis Using Parsimony is a computational phylogenetics program for inferring evolutionary trees |
4 | ✔Yes | ||
PBJELLY | Highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles |
15.8.24 | ✔Yes | Genome assembly workshop | |
perl | Programming language | ✔Yes | Arkansas Workshop, | ||
phenix | For reference mapping, VCF genearation, VCF filtering, and SNP identification |
4-Jan | ✔Yes | ||
phylip | PHYLogeny Inference Package | 3.69 | ✔Yes | ✔Yes | |
Phylosift | Tool suite to conduct phylogenetic analysis of genomes and metagenomes |
1.0.1 | ✔Yes | ||
picard | Manipulating high-throughput sequencing (HTS) data and formats. |
2.14.0 | ✔Yes | Genomics Toolkit | |
2.17.0 | ✔Yes | ||||
2.1.1 | ✔Yes | ||||
2.18.0 | ✔Yes | ||||
2.20.2 | ✔Yes | ||||
Pilon | Automatically improves draft assemblies and finds variation among strains, including large event detection |
1.16 | ✔Yes | ||
1.23 | ✔Yes | ||||
Platanus | De novo sequence assembler for NGS data |
1.2.4 | ✔Yes | ||
plink | Open-source C/C++ library for working with human genetic variation data |
2 | ✔Yes | ||
polyphen | Automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein |
2.2.2 | ✔Yes | ||
Pplacer | Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment |
1.1.7 | ✔Yes | ||
Prinseq | Quality control for high-throughput sequence data |
1.2 | ✔Yes | Arkansas Workshop | |
Prokka | Software tool for rapid annotation of prokaryotic genomes |
1.11 | ✔Yes | ||
Prodigal | Fast, reliable protein-coding gene prediction for prokaryotic genomes |
2.6.2 | ✔Yes | ||
2.6.3 | ✔Yes | ||||
psi4 | PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms |
1.1 | ✔Yes | ✔Yes | |
Python | Programming language | ✔Yes | Arkansas Workshop | ||
QIIME2 | Quantitative Insights Into Microbial Ecology |
2.0.0 | QIIME2 | ||
QUAST | Assembly evaluation tool | 4.6.3 | ✔Yes | ||
5.0.0 | ✔Yes | ||||
R | Statistical computing and graphics |
3.2.3 | ✔Yes | ||
Rstudio | Open-source integrated development environment (IDE) for R, a programming language for statistical computing and graphics. |
3.3.1 | ✔Yes | ||
3.3.3 | ✔Yes | ||||
3.4.1 | ✔Yes | ||||
3.5.1 | ✔Yes | ||||
3.5.2 | ✔Yes | ||||
3.6.0 | ✔Yes | ||||
raxml | Maximum likelihood phylogeny estimation for interpreting relationships between sets of data |
8.0.26 | Genomics Toolkit | ||
8.2.11 | ✔Yes | ||||
8.2.9 | ✔Yes | ||||
Raxml-ng | Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. |
0.9.0 | ✔Yes | ||
0.9.0-pthreads | ✔Yes | ||||
Ray | Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data |
2.3.1 | ✔Yes | ✔Yes | |
repeatmasker | Screens DNA sequences for interspersed repeats and low complexity DNA sequences |
4.0.7 | ✔Yes | ||
4.0.6 | ✔Yes | ||||
repeatmodeler | Screens DNA sequences for interspersed repeats and low complexity DNA sequences |
1.0.10 | ✔Yes | ||
rmats | Computational tool to detect differential alternative splicing events from RNA-Seq data |
3.2.5 | ✔Yes | ||
4.0.2 | ✔Yes | ||||
RNAmmer | Predicts 5s/ s, 16s/1 s, and 23s/2 s ribosomal RNA in full genome sequences |
1.2 | ✔Yes | ||
rosetta | Software suite including algorithms for computational modeling and analysis of protein structures |
3.7 | ✔Yes | ||
3.1 | ✔Yes | ||||
rsem | Estimates gene and isoform expression levels from RNA-Seq data |
1.2.21 | ✔Yes | ||
1.3.0 | ✔Yes | ||||
sailfish | Alignment-free isoform quantification from RNA-seq reads using lightweight algorithms |
0.9.2 | ✔Yes | ||
salmon | Tool for fast transcript quantification from RNA-seq data |
0.4.2 | bcbio-nextgen toolkit v.2.0 | ||
0.6.0 | ✔Yes | ||||
0.7.2 | ✔Yes | ||||
0.8.1 | ✔Yes | ||||
0.11.0 | ✔Yes | ||||
0.9.1 | ✔Yes | ✔Yes | |||
samtools | Utilities for manipulating alignments in SAM format |
1.3 | ✔Yes | ||
1.3.1 | ✔Yes | ||||
1.5 | ✔Yes | ||||
1.9 | ✔Yes | ✔Yes | |||
1.7 | ✔Yes | ||||
Seqtk | Toolkit for processing sequences in FASTA/Q formats |
1.2-r94 | ✔Yes | ||
SignalP | Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes and eukaryotes |
4.1c | ✔Yes | ||
skmer | Estimating distances between genomes from low-coverage sequencing reads |
3.0.1 | ✔Yes | ||
SNVMIX | Detects single nucleotide variants from next generation sequencing data |
0.11.8-r5 | ✔Yes | ||
smrt | Automated and distributed secondary analysis of sequencing data generated by the PacBio single-molecule, real-time (SMRT) sequencing system |
2.2.0 | PacBio SMRT analysis | ||
5.1.0 | ✔Yes | ||||
7.0.1 | ✔Yes | ||||
somaticsniper | SomaticSniper is a program to identify single nucleotide positions that are different between tumor and norma |
1.0.5 | ✔Yes | ||
soapdenovo | De novo assembler for next generation sequencing reads |
9/10/2015 | ✔Yes | ||
2.04 | ✔Yes | ||||
soapdenovotrans | A de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level |
1.03 | ✔Yes | ||
solar eclipse | SOLAR-Eclipse is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening |
8.1.1 | bcbio-nextgen toolkit v.2.0 | ||
spades | St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies |
3.10.1 | ✔Yes | ✔Yes | Genomics Toolkit |
3.11.1 | ✔Yes | ✔Yes | |||
3.8.1 | ✔Yes | ||||
spm | Statistical Parametric Mapping | ✔Yes | |||
12 | ✔Yes | ||||
sra-toolkit | Collection of tools and libraries for using data in the INSDC Sequence Read Archives |
2.3.5-2 | Mining SRA to identify datasets | ||
2.8.1 | ✔Yes | ||||
2.8.2 | ✔Yes | ||||
2.9.1 | ✔Yes | ||||
stacks | A modular pipeline for building loci from short-read sequences |
1.48 | ✔Yes | ||
2.41 | ✔Yes | ||||
star | Spliced Transcripts Alignment to a Reference |
2.5.3 | ✔Yes | Genomics Toolkit | |
2.6.1a | ✔Yes | ||||
2.5.2 | ✔Yes | ||||
2.5.4 | ✔Yes | ||||
2.7.0 | ✔Yes | ||||
Strelka | Somatic variant calling workflow for matched tumor-normal samples |
1.0.01 | ✔Yes | ||
starfusion | Spliced Transcripts Alignment to a Reference |
1.1.0 | ✔Yes | ✔Yes | |
1.3.1 | ✔Yes | ||||
1.5.0 | ✔Yes | ||||
stringtie | Fast and highly efficient assembler of RNA sequence alignments into potential transcripts |
1.3.3b | ✔Yes | ✔Yes | Genomics Toolkit |
Supernova | Supernova is a software package from 10X Genomics for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source |
0.2.6 | Genome assembly workshop | ||
tabix | Tabix works on generic tabular data formats for genomic information, quickly retrieving features overlapping specified areas on the genome |
0.26 | ✔Yes | Genomics Toolkit | |
Tcoffee | Multiple Sequence Alignment Server |
Genomics Toolkit | |||
Theano | Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently |
0.8.0 | ✔Yes | ||
0.8.2 | ✔Yes | ||||
TMHMM | Predicts transmembrane helices in proteins |
2 | ✔Yes | bcbio-nextgen toolkit v.2.0 | |
tophat | Fast splice junction mapper for RNA-Seq reads |
2.0.7 | Genomics Toolkit | ||
2.1.0 | ✔Yes | ||||
2.1.1 | ✔Yes | ✔Yes | |||
tophat2 | Splice junction mapper for RNA-Seq reads |
4.6.2 | bcbio-nextgen toolkit v.2.0, | ||
2.1.1 | ✔Yes | ||||
transabyss | Analysis for ABySS-assembled contigs from shotgun transcriptome data for finding splice sites and variants |
1.0.3 | |||
1.5.5 | ✔Yes | ||||
2.0.1 | ✔Yes | ✔Yes | |||
transdecoder | TransDecoder identifies candidate coding regions within transcript sequences |
3.0.1 | ✔Yes | ||
Transrate | Software for de-novo transcriptome assembly quality analysis |
1.0.3 | ✔Yes | ✔Yes | |
trim galore | A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files |
2.1.1 | Arkansas Workshop | ||
0.4.5 | ✔Yes | ✔Yes | |||
0.6.3 | ✔Yes | ||||
trimmomatic | Fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. |
0.36 | ✔Yes | ✔Yes | Genomics Toolkit |
trinity | Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data |
2.3.2 | ✔Yes | Arkansas Workshop | |
2.4.0 | ✔Yes | ✔Yes | |||
2.0.1 | |||||
2.6.6 | ✔Yes | ||||
2.8.4 | ✔Yes | ✔Yes | |||
2.1.1 | ✔Yes | ||||
2.0.6 | ✔Yes | ||||
2.2.0 | ✔Yes | ||||
Trinotate | Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms |
3.1.1 | ✔Yes | ✔Yes | |
2.0.2 | ✔Yes | ||||
Tombo | Modified nucleotides from nanopore sequencing data |
1.5 | ✔Yes | ||
vcftools | Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files |
0.1.14 | |||
0.1.13 | ✔Yes | ||||
0.1.17 | ✔Yes | ||||
0.1.15 | ✔Yes | ||||
velvet | De novo genomic assembler specially designed for short read sequencing technologies |
1.21 | ✔Yes | ✔Yes | |
warbleR | Bioacoustics research encompasses a wide range of questions, study systems and methods, including the software used for analyses. |
Harvesting Field Station Data |