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http://sourceforge.net/projects/mirdeepstar/

An integrated application software tool for miRNA identification from RNA sequencing data.

Proper citation: miRDeep* (RRID:SCR_012960) Copy   

•   Source: SciCrunch Registry

http://www.genomic.ch/edena.php

Software providing a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization.

Proper citation: Edena v3 (RRID:SCR_013065) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/amos/

A collection of tools and class interfaces for the assembly of DNA reads.

Proper citation: AMOS (RRID:SCR_013067) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/contrail-bio/

A Hadoop based genome assembler for assembling large genomes in the clouds.

Proper citation: Contrail (RRID:SCR_013066) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/ngopt/wiki/A5PipelineREADME

A pipeline for assembling DNA sequence data generated on the Illumina sequencing platform.

Proper citation: A5 (RRID:SCR_013068) Copy   

•   Source: SciCrunch Registry

http://aluru-sun.ece.iastate.edu/doku.php?id=reptile

A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.

Proper citation: Reptile (RRID:SCR_013075) Copy   

•   Source: SciCrunch Registry

http://easyfig.sourceforge.net/

A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

Proper citation: Easyfig (RRID:SCR_013169) Copy   

•   Source: SciCrunch Registry

http://microbiomeutil.sourceforge.net/#A_CS

A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/telescoper/

An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.

Proper citation: Telescoper (RRID:SCR_013206) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/palfinder/

A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.

Proper citation: palfinder (RRID:SCR_013174) Copy   

•   Source: SciCrunch Registry

http://alumni.cs.ucr.edu/~liw/isolasso.html

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

Proper citation: IsoLasso (RRID:SCR_013176) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/samcomp/

A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.

Proper citation: sam comp (RRID:SCR_013179) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/heuraa/

Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Proper citation: HeurAA (RRID:SCR_013212) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bisreadmapper/

Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.

Proper citation: bisReadMapper (RRID:SCR_013171) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~fsun/Programs/CEDER/CEDERmain.html

R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.

Proper citation: CEDER (RRID:SCR_013255) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/quantisnp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development.

Proper citation: QuantiSNP (RRID:SCR_013091) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/celeragb/

Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006.

Proper citation: Celera Genome Browser (RRID:SCR_013093) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~liangche/software.html

A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GPSeq (RRID:SCR_013250) Copy   

•   Source: SciCrunch Registry

http://bioinfo.ctb.pku.edu.cn/MAP/

This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAP (RRID:SCR_013216) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/DiffSplice

The Genome-Wide Detection of Differential Splicing Events with RNA-seq.

Proper citation: DiffSplice (RRID:SCR_013215) Copy   

•   Source: SciCrunch Registry