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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
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
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
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
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
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
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
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
A scalable software pipeline for whole genome resequencing analysis.
Proper citation: Crossbow (RRID:SCR_013306) Copy
http://tomcatbackup.esat.kuleuven.be/inclusive/
A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
Proper citation: INCLUSive (RRID:SCR_013488) Copy
http://hannonlab.cshl.edu/Alta-Cyclic/main.html
An Illumina Genome-Analyzer (Solexa) base caller.
Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy
American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.
Proper citation: Google (RRID:SCR_017097) Copy
https://laniakea-elixir-it.github.io/
Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.
Proper citation: Laniakea (RRID:SCR_018146) Copy
http://www.bioconductor.org/packages/release/bioc/html/iontree.html
Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Proper citation: iontree (RRID:SCR_002813) Copy
https://github.com/telatin/covtobed
Software tool to generate BED coverage tracks from BAM files.
Proper citation: covtobed (RRID:SCR_023998) Copy
https://www.gnumed.de/documentation/
Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.
Proper citation: GNUmed (RRID:SCR_024029) Copy
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Proper citation: Chemtool (RRID:SCR_023992) Copy
Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer.
Proper citation: Entangle (RRID:SCR_024015) Copy
https://sourceforge.net/projects/ffp-phylogeny/
Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison.
Proper citation: FFP (RRID:SCR_024018) Copy
https://github.com/danielhuson/dendroscope3
Software Java program for analyzing and visualizing rooted phylogenetic trees and networks.
Proper citation: Dendroscope3 (RRID:SCR_024003) Copy
https://github.com/GregoryFaust/yaha
Software tool as fast and flexible long read alignment with optimal breakpoint detection.
Proper citation: yaha (RRID:SCR_024365) Copy
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