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http://www.broadinstitute.org/cancer/cga/contest

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

Proper citation: ContEst (RRID:SCR_000595) Copy   

•   Source: SciCrunch Registry

Discontinued

https://github.com/PacificBiosciences/blasr

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLASR (RRID:SCR_000764) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmcloser/

Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

Proper citation: GMcloser (RRID:SCR_000646) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fastuniq/

A software tool for removal of de novo duplicates in paired short DNA sequences.

Proper citation: FastUniq (RRID:SCR_000682) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4474950

A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.

Proper citation: Sequencing Analysis Software (RRID:SCR_000718) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-toolbox/

A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.

Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/operasf/

A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

Proper citation: Opera (RRID:SCR_000665) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/rmap/

Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.

Proper citation: RMAP (RRID:SCR_000695) Copy   

•   Source: SciCrunch Registry

https://github.com/iontorrent/TMAP

Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

Proper citation: TMAP (RRID:SCR_000687) Copy   

•   Source: SciCrunch Registry

http://www.frontiersci.com/

A commercial vendor of chemicals that provides custom synthesis of a wide variety of organic compounds. Frontier Scientific has capabilities for custom work in organoborons, organotins, porphyrins, silanes, halogenations, catalysts and cross couplings using Suzuki, Stille, and Kumada processes.

Proper citation: Frontier Scientific Chemical Supplier (RRID:SCR_000914) Copy   

•   Source: SciCrunch Registry

http://www.dundee.ac.uk/

University in Scotland, UK that provides undergraduate and doctoral degree programs.

Proper citation: University of Dundee; Scotland; United Kingdom (RRID:SCR_000997) Copy   

•   Source: SciCrunch Registry

http://www.tufts.edu/

Private research university in Medford and Somerville, Massachusetts, United States, with additional facilities in Boston and Grafton, as well as Talloires, France. Provides undergraduate, graduate, and professional degree programs.

Proper citation: Tufts University; Massachusetts; USA (RRID:SCR_000994) Copy   

•   Source: SciCrunch Registry

http://www.pasteur-lille.fr/

Pasteur Institute of Lille is an international research institute in Lille, France focused on bettering human health by detecting risk factors in degenerative diseases.

Proper citation: Pasteur Institute of Lille; Lille; France (RRID:SCR_000990) Copy   

•   Source: SciCrunch Registry

http://www.ced.co.uk/pru.shtml?spk7wglu.htm

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. A data acquisition and analysis software package for electrophysiology data. Spike2 software offers multi-channel continuous data acquisition and analysis with a multitude of options. This offers flexible usage from a simple chart recorder to complex applications requiring stimulus generation, data capture, scrolling or triggered displays, control of external equipment, and custom analysis. Spike2 software can be used in many fields such as electrophysiology, neurophysiology, cardiovascular and respiratory studies, sports science and pharmacology.

Proper citation: Spike2 Software (RRID:SCR_000903) Copy   

•   Source: SciCrunch Registry

http://orwh.od.nih.gov/

The Office of Research on Women's Health (ORWH) is part of the Office of the Director of NIH. ORWH works in partnership with the 27 NIH Institutes and Centers to ensure that women’s health research is part of the scientific framework at the NIH and throughout the scientific community.

Proper citation: NIH Office of Research on Women's Health; Bethesda; Maryland (RRID:SCR_000986) Copy   

•   Source: SciCrunch Registry

http://www.ntu.edu.tw/english/

A national research university in Taipei, Taiwan. The university confers degrees at the undergraduate and graduate level bio-resources and agriculture, electrical engineering and computer science, engineering, law, liberal arts, management, medicine, public health, and the social sciences.

Proper citation: National Taiwan University; Taipei; Taiwan (RRID:SCR_000983) Copy   

•   Source: SciCrunch Registry

http://www.nus.edu.sg

A public university located in Singapore that has a wide range of faculties and schools, including arts, business, computing, and dentistry.

Proper citation: National University of Singapore; Singapore; Singapore (RRID:SCR_000984) Copy   

•   Source: SciCrunch Registry

http://cryptogenome.ucsf.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco

Proper citation: CryptoBase (RRID:SCR_000780) Copy   

•   Source: SciCrunch Registry

http://www.filemaker.com

A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline.

Proper citation: FileMaker (RRID:SCR_000783) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/glycoworkbench/

A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.

Proper citation: GlycoWorkbench (RRID:SCR_000782) Copy   

•   Source: SciCrunch Registry