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A generic sequence comparison tool for visualizing genome alignments both within and between species.
Proper citation: SynBrowse (RRID:SCR_011807) Copy
http://code.google.com/p/condetri/
Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.
Proper citation: ConDeTri (RRID:SCR_011838) Copy
http://www.cbcb.umd.edu/software/quake/
A software package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
Proper citation: Quake (RRID:SCR_011839) Copy
Software providing a framework for collecting, storing, and accessing data produced by a wide variety of experiments.
Proper citation: SBEAMS (RRID:SCR_011830) Copy
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.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://code.google.com/p/discovering-cse/
Software for discovering motifs that induce sequencing errors.
Proper citation: discovering-cse (RRID:SCR_011832) 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://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
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://www.cse.sc.edu/~elallali/research/MGC.html
A software application for finding complete and incomplete genes in metagenomic reads.
Proper citation: MGC (RRID:SCR_011935) Copy
http://ab.inf.uni-tuebingen.de/software/metasim/
A Sequencing Simulator for Genomics and Metagenomics.
Proper citation: MetaSim (RRID:SCR_011940) Copy
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