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https://gitlab.sib.swiss/EPD/chipseq
Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.
Proper citation: ChIP-seq (RRID:SCR_001237) Copy
http://sourceforge.net/projects/ngsrich/
Software for target enrichment performance for next-generation sequencing.
Proper citation: NGSrich (RRID:SCR_001333) Copy
http://sourceforge.net/projects/pasha/
A parallel short read assembler for large genomes using de Bruijn graphs.
Proper citation: PASHA (RRID:SCR_004455) Copy
http://mged.sourceforge.net/ontologies/MGEDontology.php
An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.
Proper citation: MGED Ontology (RRID:SCR_004484) Copy
http://snoopcgh.sourceforge.net/
A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.
Proper citation: SnoopCGH (RRID:SCR_004420) Copy
https://computation-rnd.llnl.gov/lmat/
Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.
Proper citation: LMAT (RRID:SCR_004646) Copy
A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
Proper citation: USeq (RRID:SCR_004753) Copy
http://svmerge.sourceforge.net/
Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.
Proper citation: SVMerge (RRID:SCR_004777) Copy
http://petrov.stanford.edu/cgi-bin/Tlex.html
Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.
Proper citation: T-lex (RRID:SCR_005134) Copy
http://sourceforge.net/projects/cohcap/
An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.
Proper citation: COHCAP (RRID:SCR_006499) Copy
http://sourceforge.net/projects/dtailor/
A fully extendable software framework, for property-based design of synthetic DNA sequences.
Proper citation: D-Tailor (RRID:SCR_000115) Copy
http://sourceforge.net/projects/sirnarules/
An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.
Proper citation: siRNArules (RRID:SCR_000096) Copy
http://sourceforge.net/projects/abmining/
Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).
Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy
http://sourceforge.net/projects/spdesigner/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.
Proper citation: SP-Designer (RRID:SCR_000031) Copy
http://sourceforge.net/projects/mysirna/
Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.
Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy
http://sourceforge.net/projects/dprimer/
A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
Proper citation: dprimer (RRID:SCR_000050) Copy
http://sourceforge.net/projects/imethy/
Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.
Proper citation: iMethy (RRID:SCR_000049) Copy
http://sourceforge.net/projects/protms/
A software tool for the proteomics community that may help improving analysis of proteomic experimental data.
Proper citation: Quant (RRID:SCR_000267) Copy
http://sourceforge.net/projects/biogrinder/
An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
Proper citation: Grinder (RRID:SCR_000168) Copy
A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.
Proper citation: GProX (RRID:SCR_000273) Copy
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