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http://mmb.pcb.ub.es/nucleR/

A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

Proper citation: nucleR (RRID:SCR_010895) 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://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm

A robust software package for quantitative comparison of ChIP-Seq data sets.

Proper citation: MAnorm (RRID:SCR_010869) Copy   

•   Source: SciCrunch Registry

http://software.big.ac.cn/MeRIP-PF.html

A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.

Proper citation: MeRIP-PF (RRID:SCR_010904) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/batmeth/

Improved mapper for bisulfite sequencing reads on DNA methylation.

Proper citation: BatMeth (RRID:SCR_010906) Copy   

•   Source: SciCrunch Registry

http://quma.cdb.riken.jp/

You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.

Proper citation: QUMA (RRID:SCR_010907) 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

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   

•   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://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://bioinformatics.rutgers.edu/Software/SLiQ/

Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph.

Proper citation: SLIQ (RRID:SCR_005003) Copy   

•   Source: SciCrunch Registry

http://www.physics.rutgers.edu/~anirvans/SOPRA/

Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD.

Proper citation: SOPRA (RRID:SCR_005035) Copy   

•   Source: SciCrunch Registry

http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/

A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.

Proper citation: SSPACE (RRID:SCR_005056) Copy   

•   Source: SciCrunch Registry

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

Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data.

Proper citation: MBCluster.Seq (RRID:SCR_005079) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexeyG/GRASS

A generic algorithm for scaffolding next-generation sequencing assemblies.

Proper citation: GRASS (RRID:SCR_005071) Copy   

•   Source: SciCrunch Registry

http://www.comp.hkbu.edu.hk/~chxw/software/G-BLASTN.html

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.

Proper citation: G-BLASTN (RRID:SCR_005062) Copy   

•   Source: SciCrunch Registry

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://yost.genetics.utah.edu/software.php

A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants.

Proper citation: MMAPPR (RRID:SCR_005092) Copy   

•   Source: SciCrunch Registry

http://www.omicsoft.com/fusionmap/

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI.

Proper citation: FusionMap (RRID:SCR_005242) Copy   

•   Source: SciCrunch Registry

http://www.raetschlab.org/suppl/rquant

Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts.

Proper citation: rQuant (RRID:SCR_005150) Copy   

•   Source: SciCrunch Registry