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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
https://github.com/hyattpd/Prodigal
Software tool for protein coding gene prediction for prokaryotic genomes.
Proper citation: Prodigal (RRID:SCR_011936) 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://opal.biology.gatech.edu/GeneMark/
A family of gene prediction programs developed at Georgia Institute of Technology.
Proper citation: GeneMark (RRID:SCR_011930) 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
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://artiva.gene-networks.net/artiva-2/
Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks.
Proper citation: ARTIVA (RRID:SCR_011946) Copy
http://cbcb.umd.edu/software/metAMOS
A modular and open source metagenomic assembly and analysis pipeline.
Proper citation: MetAMOS (RRID:SCR_011914) 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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