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https://github.com/ding-lab/msisensor

A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.

Proper citation: MSIsensor (RRID:SCR_006418) Copy   

•   Source: SciCrunch Registry

http://www.clipz.unibas.ch/downloads/TSSer/index.php

A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide.

Proper citation: TSSer (RRID:SCR_006419) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/wanding/duprecover/overview

Software that facilitates accurate estimation for sampling-induced read duplication in deep sequencing experiments.

Proper citation: DupRecover (RRID:SCR_006410) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/socrates/

Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.

Proper citation: Socrates (RRID:SCR_006411) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

Proper citation: AbsCN-seq (RRID:SCR_006409) Copy   

•   Source: SciCrunch Registry

http://folk.uio.no/einarro/Projects/KFM-index/

Provides a compact storage of de Bruijn subgraphs representing the k-subwords of a set of strings.

Proper citation: kFM-index (RRID:SCR_006435) Copy   

•   Source: SciCrunch Registry

http://webdav.tuebingen.mpg.de/u/karsten/Forschung/research.html?page=research&topic=SV-M&html=text

Software for accurate indel prediction using paired-end short reads.

Proper citation: SV-M (RRID:SCR_006461) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/saap-rrbs/

Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing.

Proper citation: SAAP-RRBS (RRID:SCR_006516) Copy   

•   Source: SciCrunch Registry

http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format.

Proper citation: ART (RRID:SCR_006538) Copy   

•   Source: SciCrunch Registry

http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/Bioinfotools/NGS/website/index.php

Computational-based software that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.

Proper citation: NGS-QC Generator (RRID:SCR_006536) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cohcap/

An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Proper citation: COHCAP (RRID:SCR_006499) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/htSeqTools.html

Software tools for quality control, visualization and processing for High-Throughput Sequencing data. These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.

Proper citation: htSeqTools (RRID:SCR_006614) Copy   

•   Source: SciCrunch Registry

http://bioinfo.lifl.fr/yass/iedera_solid/storm/

A software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SToRM (RRID:SCR_006696) Copy   

•   Source: SciCrunch Registry

http://garm-meta-assem.sourceforge.net/

A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

Proper citation: GARM (RRID:SCR_006731) Copy   

•   Source: SciCrunch Registry

http://sammeth.net/confluence/display/FLUX/Home

Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.

Proper citation: FLUX CAPACITOR (RRID:SCR_006651) Copy   

•   Source: SciCrunch Registry

https://github.com/nariai/tigar

Software to estimate transcript isoform abundances from RNA-Seq data by variational Bayesian inference. The statistical method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads.

Proper citation: TIGAR (RRID:SCR_006650) Copy   

•   Source: SciCrunch Registry

http://compbio.bccrc.ca/software/apolloh/

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

Proper citation: APOLLOH (RRID:SCR_006648) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/samscope/

A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.

Proper citation: Samscope (RRID:SCR_006715) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dmeas/

A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.

Proper citation: DMEAS (RRID:SCR_006679) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/DeconRNASeq.html

An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

Proper citation: DeconRNASeq (RRID:SCR_006713) Copy   

•   Source: SciCrunch Registry