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http://www.embl.de/~korbel/CopySeq/

A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.

Proper citation: CopySeq (RRID:SCR_010758) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ekg/freebayes

A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

Proper citation: FreeBayes (RRID:SCR_010761) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/pvac.html

Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

Proper citation: pvac (RRID:SCR_000359) Copy   

•   Source: SciCrunch Registry
  

https://github.com/GregoryFaust/samblaster

Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

Proper citation: SAMBLASTER (RRID:SCR_000468) Copy   

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http://nmrml.org/

An open mark-up language for NMR data.

Proper citation: nmrML (RRID:SCR_000467) Copy   

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http://www.tapyr.net/

An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.

Proper citation: TAPyR (RRID:SCR_000588) Copy   

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http://sourceforge.net/projects/microanalyzer/

Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.

Proper citation: Micro-Analyzer (RRID:SCR_000394) Copy   

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http://sourceforge.net/projects/srma/

A post-alignment micro re-aligner for next-generation high throughput sequencing data.

Proper citation: SRMA (RRID:SCR_000669) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/rbsurv.html

Software package that selects genes associated with survival.

Proper citation: rbsurv (RRID:SCR_001175) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/wateRmelon.html

Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

Proper citation: wateRmelon (RRID:SCR_001296) Copy   

•   Source: SciCrunch Registry
  

https://github.com/FelixKrueger/Sherman

Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.

Proper citation: Sherman (RRID:SCR_001294) Copy   

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http://yiplab.cse.cuhk.edu.hk/probrna/

Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

Proper citation: ProbRNA (RRID:SCR_001288) Copy   

•   Source: SciCrunch Registry
  

http://www.bioinformatics.org/peakanalyzer/wiki/

A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

Proper citation: PeakAnalyzer (RRID:SCR_001194) Copy   

•   Source: SciCrunch Registry
  

http://sv.gersteinlab.org/breakseq/

Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR).

Proper citation: BreakSeq (RRID:SCR_001186) Copy   

•   Source: SciCrunch Registry
  

http://www-genepi.med.utah.edu/suppl/SLOPE/index.html

Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SLOPE (RRID:SCR_001185) Copy   

•   Source: SciCrunch Registry
  

http://genomics1.mh-hannover.de/genometa/index.php?Site=Home

A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of.

Proper citation: Genometa (RRID:SCR_001181) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cuda-ec/

A fast parallel error correction tool for short reads.

Proper citation: CUDA-EC (RRID:SCR_001090) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/ibm-cbc-genomic-tools/

A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.

Proper citation: GenomicTools (RRID:SCR_001205) Copy   

•   Source: SciCrunch Registry
  

http://www.genome.duke.edu/labs/ohler/research/PARalyzer/

Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

Proper citation: PARalyzer (RRID:SCR_001208) Copy   

•   Source: SciCrunch Registry
  

https://vcftools.github.io/index.html

Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.

Proper citation: VCFtools (RRID:SCR_001235) Copy   

•   Source: SciCrunch Registry