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http://sourceforge.net/projects/aeo/

AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms

Proper citation: Adverse Event Ontology (RRID:SCR_006807) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gbsbarcode/

PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported.

Proper citation: GBS barcode splitter (RRID:SCR_006799) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamstats/

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

Proper citation: BAMStats (RRID:SCR_006973) Copy   

•   Source: SciCrunch Registry

http://seqbarracuda.sourceforge.net/

A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.

Proper citation: BarraCUDA (RRID:SCR_006881) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/taipan/

A fast hybrid short-read assembly tool.

Proper citation: Taipan (RRID:SCR_007330) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://brig.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://snp-magma.sourceforge.net

Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem.

Proper citation: MAGMA (RRID:SCR_005757) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-toolbox/

A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.

Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/operasf/

A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

Proper citation: Opera (RRID:SCR_000665) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phaccs/

Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.

Proper citation: PHACCS (RRID:SCR_001232) Copy   

•   Source: SciCrunch Registry

http://bioinf.spbau.ru/quast

Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.

Proper citation: QUAST (RRID:SCR_001228) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kanalyze/

A Java toolkit designed to convert DNA and RNA sequences into k-mers.

Proper citation: KAnalyze (RRID:SCR_001323) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dical-ibd/

Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.

Proper citation: diCal-IBD (RRID:SCR_012111) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ionwinze/

Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.

Proper citation: Ionwinze (RRID:SCR_012115) Copy   

•   Source: SciCrunch Registry