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http://sourceforge.net/projects/viralfusionseq/

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.

Proper citation: VFS (RRID:SCR_005138) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cova/

A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype.

Proper citation: COVA (RRID:SCR_005175) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qure/

A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.

Proper citation: QuRe (RRID:SCR_005209) Copy   

•   Source: SciCrunch Registry

http://orman.sourceforge.net/Home

A software tool for resolving multi-mappings within an RNA-Seq SAM file.

Proper citation: ORMAN (RRID:SCR_005188) Copy   

•   Source: SciCrunch Registry

http://ergatis.sourceforge.net/

A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.

Proper citation: Ergatis (RRID:SCR_005377) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/molbiolib/

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.

Proper citation: MolBioLib (RRID:SCR_005372) Copy   

•   Source: SciCrunch Registry

http://splitread.sourceforge.net/

Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data.

Proper citation: SPLITREAD (RRID:SCR_005264) Copy   

•   Source: SciCrunch Registry

http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

http://chipexo.sourceforge.net/

A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching.

Proper citation: MACE (RRID:SCR_005520) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/treq/home/Home/

A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.

Proper citation: TreQ (RRID:SCR_005505) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/netclassr/

An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM).

Proper citation: netClass (RRID:SCR_005672) Copy   

•   Source: SciCrunch Registry

http://tmaj.pathology.jhmi.edu/

Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.

Proper citation: TMAJ (RRID:SCR_005601) Copy   

•   Source: SciCrunch Registry

http://staden.sourceforge.net/

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Proper citation: Staden Package (RRID:SCR_005629) 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://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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://genovar.sourceforge.net/

A Detection and Visualization software tool for Genomic Variants.

Proper citation: Genovar (RRID:SCR_010930) Copy   

•   Source: SciCrunch Registry

http://ranger.sourceforge.net/

Software for a multi-purpose ChIP Seq peak caller.

Proper citation: PeakRanger (RRID:SCR_010863) Copy   

•   Source: SciCrunch Registry