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http://www.mhh.de/acghtool.html

A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs.

Proper citation: aCGHtool (RRID:SCR_010915) Copy   

•   Source: SciCrunch Registry

https://earray.chem.agilent.com/cghanalytics/index.html

A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.

Proper citation: Agilent Genomic Workbench (RRID:SCR_010918) Copy   

•   Source: SciCrunch Registry

http://pages.cs.wisc.edu/~kliang/DBChIP/

Detects differential binding of transcription factors with ChIP-seq.

Proper citation: DBChIP (RRID:SCR_010872) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/DIME/index.html

R-package for identifying differential ChIP-seq based on an ensemble of mixture models.

Proper citation: DIME (RRID:SCR_010874) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucf.edu/~xiaoman/ChIPModule/ChIPModule.html

A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.

Proper citation: ChIPModule (RRID:SCR_010877) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://erne.sourceforge.net/

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   

•   Source: SciCrunch Registry

http://fureylab.web.unc.edu/software/fseq/

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

Proper citation: F-Seq (RRID:SCR_010880) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/ea-utils/

Command-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

Proper citation: ea-utils (RRID:SCR_005553) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bseqc/

A quality control software package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.

Proper citation: BSeQC (RRID:SCR_005428) Copy   

•   Source: SciCrunch Registry

http://brainarray.mbni.med.umich.edu/brainarray/ngsqc/

Software pipeline that provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequences, are not caused by low quality sequencing.

Proper citation: NGSQC (RRID:SCR_005459) Copy   

•   Source: SciCrunch Registry

http://www.stat.purdue.edu/~cheng70/code.html

A classification software for DNA methylation profiling with bisulphite next-generation sequencing data.

Proper citation: MSC (RRID:SCR_005450) Copy   

•   Source: SciCrunch Registry

http://smithlab.usc.edu/plone/software/mlml

A software tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments. It generates consistent estimates across experiment types.

Proper citation: MLML (RRID:SCR_005449) Copy   

•   Source: SciCrunch Registry

http://bioinfo2.ugr.es/MethylExtract/

A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.

Proper citation: MethylExtract (RRID:SCR_005446) Copy   

•   Source: SciCrunch Registry

http://campagnelab.org/software/gobyweb/

Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.

Proper citation: GobyWeb (RRID:SCR_005443) Copy   

•   Source: SciCrunch Registry

http://www.computationalbioenergy.org/qc-chain.html

A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data.

Proper citation: QC-Chain (RRID:SCR_005438) Copy   

•   Source: SciCrunch Registry

https://github.com/laserson/vdj

Python package for analysing immune receptor sequences (antibodies and T cell receptors).

Proper citation: VDJ (RRID:SCR_005475) Copy   

•   Source: SciCrunch Registry

http://carringtonlab.org/resources/cashx

Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G.

Proper citation: CASHX (RRID:SCR_005477) 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://diprogb.fli-leibniz.de/

Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand.

Proper citation: DiProGB (RRID:SCR_005651) Copy   

•   Source: SciCrunch Registry