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http://www.bioinformatics.babraham.ac.uk/projects/sierra/

Web based Laboratory Information Management System (LIMS) system which can be used to track samples and distribute results within small sequencing facility. Provides simple way to track samples within facility and return sequencing, mapping and QC results to users.

Proper citation: Babraham Sierra (RRID:SCR_011831) Copy   

•   Source: SciCrunch Registry

http://www.uts.edu.au/

Public research university located in Sydney, Australia.

Proper citation: University of Technology at Sydney; New South Wales; Australia (RRID:SCR_011711) Copy   

•   Source: SciCrunch Registry

http://www.h-invitational.jp/g-compass/

It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage.

Proper citation: G-compass (RRID:SCR_011799) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/discovering-cse/

Software for discovering motifs that induce sequencing errors.

Proper citation: discovering-cse (RRID:SCR_011832) Copy   

•   Source: SciCrunch Registry

https://tennessee.edu/

University of Tennessee System is comprised of campuses at Knoxville, Chattanooga, Pulaski and Martin; Health Science Center at Memphis; Space Institute at Tullahoma; and statewide Institute of Agriculture and Institute for Public Service.

Proper citation: University of Tennessee; Tennessee; USA (RRID:SCR_011712) Copy   

•   Source: SciCrunch Registry

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

A software package for building accurate ConSeqs from tagged reads.

Proper citation: MT-Toolbox (RRID:SCR_011833) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/

Allows detecting and removing multiple alien sequences in both ends of sequence reads.

Proper citation: AlienTrimmer (RRID:SCR_011835) Copy   

•   Source: SciCrunch Registry

http://www.usciences.edu/academics/collegesDepts/pcp.aspx

Pharmaceutical education began at Philadelphia College of Pharmacy (PCP), the first such institution in North America. With nearly two centuries of experience in pharmacy and science and thousands of alumni working in the healthcare industry, the world turns to PCP graduates for advice. From undergraduate majors to graduate degrees to our esteemed PharmD program, you can learn where the founders (alumni such as McNeil, Lilly, Rorer, Wyeth, Warner, Burroughs, and Wellcome) of six of the top pharmaceutical companies in the world got their education. Since 1821, they have been preparing professionals in pharmacy practice, science, and health care. There is no better place than PCP to prepare you for a lifelong career in the healthcare industry.

Proper citation: University of the Sciences in Philadelphia College of Pharmacy (RRID:SCR_011728) Copy   

•   Source: SciCrunch Registry

http://www.uttyler.edu/

Public university in Tyler, Texas. Founded in 1971, it is a part of the University of Texas System.

Proper citation: University of Texas at Tyler; Texas; USA (RRID:SCR_011720) Copy   

•   Source: SciCrunch Registry

http://hiv.sanbi.ac.za/software/qtrim

A next generation sequence quality trimming tool.

Proper citation: QTrim (RRID:SCR_011842) Copy   

•   Source: SciCrunch Registry

https://github.com/najoshi/sabre

Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.

Proper citation: sabre (RRID:SCR_011843) Copy   

•   Source: SciCrunch Registry

https://github.com/vsbuffalo/scythe

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads.

Proper citation: Scythe (RRID:SCR_011844) Copy   

•   Source: SciCrunch Registry

http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext

A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.

Proper citation: SeqtrimNEXT (RRID:SCR_011845) Copy   

•   Source: SciCrunch Registry

https://github.com/hyattpd/Prodigal

Software tool for protein coding gene prediction for prokaryotic genomes.

Proper citation: Prodigal (RRID:SCR_011936) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/~zerbino/oases/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.

Proper citation: Oases (RRID:SCR_011896) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/rnnotator

Software designed to assemble Illumina single or paired-end reads.

Proper citation: Rnnotator (RRID:SCR_011897) Copy   

•   Source: SciCrunch Registry

http://opal.biology.gatech.edu/GeneMark/

A family of gene prediction programs developed at Georgia Institute of Technology.

Proper citation: GeneMark (RRID:SCR_011930) Copy   

•   Source: SciCrunch Registry

http://genome.cshlp.org/content/20/10/1432.full

A de novo transcriptome assembly from next-generation sequencing data.

Proper citation: STM (RRID:SCR_011898) Copy   

•   Source: SciCrunch Registry

http://tophat.cbcb.umd.edu/fusion_index.html

An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.

Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/glimmer-mg/

A software system for finding genes in environmental shotgun DNA sequences.

Proper citation: Glimmer-MG (RRID:SCR_011932) Copy   

•   Source: SciCrunch Registry