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http://www.brl.bcm.tmc.edu/pash/pashDownload.rhtml

Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.

Proper citation: Pash 3.0 (RRID:SCR_004078) Copy   

•   Source: SciCrunch Registry

http://epigraph.mpi-inf.mpg.de/WebGRAPH/

A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EpiGRAPH (RRID:SCR_004326) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/insertionmapper/

A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

Proper citation: InsertionMapper (RRID:SCR_004163) Copy   

•   Source: SciCrunch Registry

https://bcbio-nextgen.readthedocs.org/en/latest/

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

Proper citation: bcbio-nextgen (RRID:SCR_004316) Copy   

•   Source: SciCrunch Registry

http://genome.gsc.riken.jp/osc/english/dataresource/

A program to eliminate artifactual reads from next-generation sequencing data sets.

Proper citation: TagDust (RRID:SCR_004175) Copy   

•   Source: SciCrunch Registry

https://www.hgsc.bcm.edu/software/mercury

An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The analysis pipeline is deployed in local hardware and the Amazon Web Services cloud via the DNAnexus platform.

Proper citation: Mercury (RRID:SCR_004231) Copy   

•   Source: SciCrunch Registry

http://cb-commander.sourceforge.net/pmwiki.php

A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline.

Proper citation: CB-Commander (RRID:SCR_004237) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/artemis/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

Proper citation: Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) Copy   

•   Source: SciCrunch Registry

http://www.ccmp.ox.ac.uk/peakdeck

A peak-calling software program for DNAseI-seq data.

Proper citation: PeaKDEck (RRID:SCR_004268) Copy   

•   Source: SciCrunch Registry

https://github.com/dsturg/Spanki

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

Proper citation: Spanki (RRID:SCR_004469) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pasha/

A parallel short read assembler for large genomes using de Bruijn graphs.

Proper citation: PASHA (RRID:SCR_004455) Copy   

•   Source: SciCrunch Registry

http://www.leonxie.com/DeepFinder.php

Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.

Proper citation: miRDeepFinder (RRID:SCR_004456) Copy   

•   Source: SciCrunch Registry

http://snoopcgh.sourceforge.net/

A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

Proper citation: SnoopCGH (RRID:SCR_004420) Copy   

•   Source: SciCrunch Registry

http://www.irisa.fr/symbiose/projects/gassst/

Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp.

Proper citation: GASSST (RRID:SCR_004413) Copy   

•   Source: SciCrunch Registry

http://bioinfo.unl.edu/raiphy.php

A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units.

Proper citation: RAIphy (RRID:SCR_004720) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/ProViDE/

A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProViDE (RRID:SCR_004709) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/souravc/compostbin

A DNA-composition-based binning algorithm for classifying metagenomic reads. It has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins.

Proper citation: CompostBin (RRID:SCR_004619) Copy   

•   Source: SciCrunch Registry

https://github.com/HIITMetagenomics/dsm-framework

Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.

Proper citation: Distributed String Mining Framework (RRID:SCR_004736) Copy   

•   Source: SciCrunch Registry

https://tobiasrausch.com/delly/

Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.

Proper citation: DELLY (RRID:SCR_004603) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry