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A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.
Proper citation: Scalable Nucleotide Alignment Program (RRID:SCR_005501) Copy
https://github.com/richardmleggett/nextclip/
A software tool for analysing reads from Long Mate Pair (LMP) libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.
Proper citation: NextClip (RRID:SCR_005465) Copy
http://www.nipgr.res.in/ngsqctoolkit.html
A software toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: NGS QC Toolkit (RRID:SCR_005461) Copy
http://www.phrap.org/consed/consed.html
A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)
Proper citation: Consed (RRID:SCR_005650) Copy
http://ngsview.sourceforge.net/
A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.
Proper citation: NGSView (RRID:SCR_005637) Copy
https://code.google.com/p/bsmap/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Short reads mapping software for bisulfite sequencing reads.
Proper citation: BSMAP (RRID:SCR_005671) Copy
http://www.webarraydb.org/webarray/index.html
An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.
Proper citation: WebArrayDB (RRID:SCR_005577) Copy
http://biostat.mc.vanderbilt.edu/wiki/Main/ASAP
Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.
Proper citation: Advanced Sequence Automated Pipeline (RRID:SCR_005578) Copy
http://samtools.sourceforge.net/tview.shtml
Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice.
Proper citation: SAMtools Text Alignment Viewer (RRID:SCR_005611) Copy
http://rafalab.jhsph.edu/bsmooth/
A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data.
Proper citation: BSmooth (RRID:SCR_005693) Copy
https://medicine.yale.edu/lab/rimm/research/software/
Software tool for biomarker assessment and outcome based cut point optimization.
Proper citation: X-Tile (RRID:SCR_005602) Copy
http://sourceforge.net/projects/cancergrid-tma/
A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis.
Proper citation: cancergrid-tma (RRID:SCR_005595) Copy
A web-based software package for comparative genomics.
Proper citation: Sybil (RRID:SCR_005593) Copy
http://www.sanger.ac.uk/resources/software/lookseq/
A web-based application for alignment visualization, browsing and analysis of genome sequence data.
Proper citation: LookSeq (RRID:SCR_005625) Copy
http://zhanglab.c2b2.columbia.edu/index.php/OLego
A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.
Proper citation: OLego (RRID:SCR_005811) Copy
http://cran.r-project.org/web/packages/aLFQ/
An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.
Proper citation: aLFQ (RRID:SCR_005925) Copy
https://code.google.com/p/pepr-chip-seq/
A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.
Proper citation: PePr (RRID:SCR_005759) Copy
http://sourceforge.net/projects/dna-bison/
Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.
Proper citation: dna-bison (RRID:SCR_005913) Copy
http://www.bioinf.uni-freiburg.de/Software/GraphProt/
Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
Proper citation: GraphProt (RRID:SCR_005842) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.
Proper citation: CLIPZ (RRID:SCR_005755) Copy
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