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http://sourceforge.net/projects/samzip/

An encoding and decoding tool for Sequence Alignment/Map (SAM) files.

Proper citation: SAMZIP (RRID:SCR_012980) Copy   

•   Source: SciCrunch Registry

http://sammate.sourceforge.net/

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

Proper citation: SAMMate (RRID:SCR_013037) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/flexbar/

Flexible barcode and adapter removal for sequencing platforms.

Proper citation: Flexbar (RRID:SCR_013001) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/shrec-ec/

A bioinformatics tool for error correction of HTS read data.

Proper citation: SHREC (RRID:SCR_013009) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hictools/

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

Proper citation: hiCtools (RRID:SCR_013010) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/locas/

A software to assemble short reads of next generation sequencing technologies at low coverage.

Proper citation: LOCAS (RRID:SCR_013064) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

•   Source: SciCrunch Registry

http://derisilab.ucsf.edu/software/price/index.html

Software for a de novo genome assembler implemented in C++.

Proper citation: PRICE (RRID:SCR_013063) Copy   

•   Source: SciCrunch Registry

http://www.nhlbi.nih.gov/about/dld/

Supports research on the causes, diagnosis, prevention, and treatment of lung diseases and sleep disorders. Research is funded through investigator-initiated and Institute-initiated grant programs and through contract programs in areas including asthma, bronchopulmonary dysplasia, chronic obstructive pulmonary disease, cystic fibrosis, respiratory neurobiology, sleep-disordered breathing, critical care and acute lung injury, developmental biology and pediatric pulmonary diseases, immunologic and fibrotic pulmonary disease, rare lung disorders, pulmonary vascular disease, and pulmonary complications of AIDS and tuberculosis. The Division is responsible for monitoring the latest research developments in the extramural scientific community as well as identifying research gaps and needs, obtaining advice from experts in the field, and implementing programs to address new opportunities. The DLD has three branches, the Airway Biology and Disease Branch, the Lung Biology and Disease Branch, and the National Center on Sleep Disorders Research.

Proper citation: NHLBI Division of Lung Diseases (RRID:SCR_013074) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain

An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.

Proper citation: OntoQuest (RRID:SCR_013281) Copy   

•   Source: SciCrunch Registry

http://www.aans.org/

The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details.

Proper citation: American Association of Neurological Surgeons (RRID:SCR_013209) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html

Software package to explore high-throughput ''C'' data such as 5C or Hi-C.

Proper citation: HiTC (RRID:SCR_013175) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/conifer/

Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.

Proper citation: CoNIFER (RRID:SCR_013213) Copy   

•   Source: SciCrunch Registry

http://rdxplorer.sourceforge.net/

A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.

Proper citation: RDXplorer (RRID:SCR_013290) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pia2/

A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.

Proper citation: PIA (RRID:SCR_013267) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/wgsim

A small tool for simulating sequence reads from a reference genome.

Proper citation: Wgsim (RRID:SCR_013269) Copy   

•   Source: SciCrunch Registry

http://tripod.nih.gov/

Tripod is a user-friendly chemical genomics browser that is currently being developed by the informatics group at the NIH Chemical Genomics Center. The main goal of Tripod is to facilitate easy access to chemical and biological data in an intuitive, user-friendly tool. To this end, the development of Tripod is inspired by the ubiquitous iTunes software, whereby browsing and managing of media contents are being adapted to chemical and biological data.

Proper citation: Tripod (RRID:SCR_013147) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/SOAPdenovo-Trans.html

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPdenovo-Trans (RRID:SCR_013268) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.ucr.edu/brat/

BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.

Proper citation: BRAT (RRID:SCR_013159) Copy   

•   Source: SciCrunch Registry