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http://www.cs.helsinki.fi/u/lmsalmel/coral/

An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.

Proper citation: Coral (RRID:SCR_011849) Copy   

•   Source: SciCrunch Registry

http://www.genome.umd.edu/quorum.html

Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.

Proper citation: QuorUM (RRID:SCR_011840) Copy   

•   Source: SciCrunch Registry

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

Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cutadapt (RRID:SCR_011841) Copy   

•   Source: SciCrunch Registry

http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

•   Source: SciCrunch Registry

http://osprey.ucalgary.ca/

Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Osprey (RRID:SCR_003627) Copy   

•   Source: SciCrunch Registry

http://srna-tools.cmp.uea.ac.uk/

Software tools for the analysis of high-throughput small RNA data.

Proper citation: UEA sRNA toolkit (RRID:SCR_003620) Copy   

•   Source: SciCrunch Registry

http://khavarilab.stanford.edu/resources.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.

Proper citation: RINS (RRID:SCR_003652) Copy   

•   Source: SciCrunch Registry

http://jexpress.bioinfo.no/site/

Gene expression analysis software using Java.

Proper citation: J-Express (RRID:SCR_003609) Copy   

•   Source: SciCrunch Registry

http://malde.org/~ketil/jatac/sources/

Software program for filtering duplicate 454 sequences by comparing flowgram information.

Proper citation: JATAC (RRID:SCR_003978) Copy   

•   Source: SciCrunch Registry

http://www.antibodyresource.com/

A complete guide to antibody research and suppliers. Serving the scientific community since 1997, the Antibody Resource Page is a guide designed by scientists for scientists to find companies that sell catalog antibodies and custom monoclonal and polyclonal antibodies. See our other pages on antibody-related databases, software, and educational websites. If you wish to suggest or update a link, please see our FAQ.

Proper citation: Antibody Resource Page (RRID:SCR_004069) Copy   

•   Source: SciCrunch Registry

http://mendel.stanford.edu/sidowlab/downloads/quest/

A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.

Proper citation: Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) Copy   

•   Source: SciCrunch Registry

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://www.ncbi.nlm.nih.gov/pmc/

Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.

Proper citation: PubMed Central (RRID:SCR_004166) 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://pubchem.ncbi.nlm.nih.gov/

Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

Proper citation: PubChem (RRID:SCR_004284) 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