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A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
Proper citation: Circos (RRID:SCR_011798) Copy
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
Public research university located in Sydney, Australia.
Proper citation: University of Technology at Sydney; New South Wales; Australia (RRID:SCR_011711) Copy
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
https://sites.google.com/site/moleculetagtoolbox/
A software package for building accurate ConSeqs from tagged reads.
Proper citation: MT-Toolbox (RRID:SCR_011833) Copy
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
http://hiv.sanbi.ac.za/software/qtrim
A next generation sequence quality trimming tool.
Proper citation: QTrim (RRID:SCR_011842) Copy
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
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
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
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
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
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
http://whale.bio.titech.ac.jp/metagene/
A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaGeneAnnotator (RRID:SCR_011934) Copy
http://ab.inf.uni-tuebingen.de/software/metasim/
A Sequencing Simulator for Genomics and Metagenomics.
Proper citation: MetaSim (RRID:SCR_011940) Copy
http://ab.inf.uni-tuebingen.de/software/megan/
Software for analyzing metagenomes.
Proper citation: MEGAN (RRID:SCR_011942) Copy
http://vm-lux.embl.de/~kultima/MOCAT//
Software package for analyzing metagenomics datasets.
Proper citation: MOCAT (RRID:SCR_011943) Copy
A clustering algorithm focusing on noise injection for subsequent cluster validation.
Proper citation: pyGCluster (RRID:SCR_011944) Copy
http://www.phrap.org/phredphrapconsed.html
A software program for assembling shotgun DNA sequence data.
Proper citation: Phrap (RRID:SCR_011917) Copy
http://denovoassembler.sourceforge.net/
Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.
Proper citation: Ray Meta (RRID:SCR_011918) Copy
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