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http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://geckoe.sourceforge.net/
A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
Proper citation: Gecko (RRID:SCR_009001) Copy
http://scalce.sourceforge.net/Home
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
Proper citation: SCALCE (RRID:SCR_009658) Copy
http://sourceforge.net/apps/mediawiki/cdao/
A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science
Proper citation: Comparative Data Analysis Ontology (RRID:SCR_010297) Copy
http://htsvipr.sourceforge.net/
A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
Proper citation: vipR (RRID:SCR_010685) Copy
http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks
Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).
Proper citation: FindPeaks (RRID:SCR_010857) Copy
http://contra-cnv.sourceforge.net/
A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
Proper citation: CONTRA (RRID:SCR_010814) Copy
http://svdetect.sourceforge.net/Site/Home.html
Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.
Proper citation: SVDetect (RRID:SCR_010812) Copy
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page
A de novo whole-genome shotgun (WGS) DNA sequence assembler.
Proper citation: Celera assembler (RRID:SCR_010750) Copy
http://dnptrapper.sourceforge.net/
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Proper citation: DNPTrapper (RRID:SCR_010981) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.
Proper citation: Hawkeye (RRID:SCR_010982) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://bio-bwa.sourceforge.net/
Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
Proper citation: BWA (RRID:SCR_010910) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
Proper citation: ERNE (RRID:SCR_010912) Copy
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