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http://www.well.ox.ac.uk/project-stampy
A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases
Proper citation: Stampy (RRID:SCR_005504) Copy
A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.
Proper citation: Scalable Nucleotide Alignment Program (RRID:SCR_005501) Copy
https://laniakea-elixir-it.github.io/
Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.
Proper citation: Laniakea (RRID:SCR_018146) Copy
https://gemini.readthedocs.io/en/latest/
Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
Proper citation: GEMINI (RRID:SCR_014819) Copy
http://www.bioconductor.org/packages/release/bioc/html/iontree.html
Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Proper citation: iontree (RRID:SCR_002813) Copy
https://github.com/telatin/covtobed
Software tool to generate BED coverage tracks from BAM files.
Proper citation: covtobed (RRID:SCR_023998) Copy
https://www.gnumed.de/documentation/
Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.
Proper citation: GNUmed (RRID:SCR_024029) Copy
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Proper citation: Chemtool (RRID:SCR_023992) Copy
Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer.
Proper citation: Entangle (RRID:SCR_024015) Copy
https://sourceforge.net/projects/ffp-phylogeny/
Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison.
Proper citation: FFP (RRID:SCR_024018) Copy
https://github.com/danielhuson/dendroscope3
Software Java program for analyzing and visualizing rooted phylogenetic trees and networks.
Proper citation: Dendroscope3 (RRID:SCR_024003) Copy
https://github.com/GregoryFaust/yaha
Software tool as fast and flexible long read alignment with optimal breakpoint detection.
Proper citation: yaha (RRID:SCR_024365) Copy
Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs.
Proper citation: zAlign (RRID:SCR_024360) Copy
https://omics.pnl.gov/software/ms-gf
Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Proper citation: MS-GF+ (RRID:SCR_015646) Copy
An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
Proper citation: RUM (RRID:SCR_008818) Copy
https://github.com/armintoepfer/QuasiRecomb/releases
A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.
Proper citation: QuasiRecomb (RRID:SCR_008812) Copy
Merging Two Gene Expression Studies via Cross Platform Normalization.
Proper citation: XPN (RRID:SCR_008845) Copy
http://tvap.genome.wustl.edu/tools/music/
A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MuSiC (RRID:SCR_008792) Copy
http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/
A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
Proper citation: SeqSaw (RRID:SCR_009185) Copy
An application for discovering potential splice junctions in high throughput sequencing (HTS) data.
Proper citation: Supersplat (RRID:SCR_009826) Copy
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