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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.
http://gaggle.systemsbiology.net/docs/geese/genomebrowser/
An open source software tool for visualizing high-density data plotted against coordinates on the genome.
Proper citation: Gaggle (RRID:SCR_011780) Copy
http://www.csd.uwo.ca/~ilie/HiTEC/
Accurate error correction in high-throughput sequencing data.
Proper citation: HiTEC (RRID:SCR_011826) Copy
https://bioinf.eva.mpg.de/patman/
Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PatMaN (RRID:SCR_011821) Copy
http://bix.ucsd.edu/projects/hammer/
A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Hammer (RRID:SCR_011825) Copy
Software for searching DNA sequence databases for RNA structure and sequence similarities.
Proper citation: Infernal (RRID:SCR_011809) Copy
http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html
A graphical interface for comparative genomics.
Proper citation: GenomeMatcher (RRID:SCR_011800) Copy
http://www-ps.informatik.uni-tuebingen.de/itNew/?page_id=1160
Alignment visualization based on SuperGenome coordinates.
Proper citation: GenomeRing (RRID:SCR_011801) Copy
An interactive, web-based tool for comparative genomic visualization.
Proper citation: Gobe (RRID:SCR_011802) Copy
http://cas-bioinfo.cas.unt.edu/gsv/homepage.php
Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them.
Proper citation: GSV (RRID:SCR_011803) Copy
http://utgenome.org/index.html
An open-source software for developing personalized genome browsers that work in web browsers.
Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy
http://graphics.med.yale.edu/trim/
A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.
Proper citation: Btrim (RRID:SCR_011836) Copy
http://www.genome.umd.edu/quorum.html
Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
Proper citation: QuorUM (RRID:SCR_011840) Copy
http://code.google.com/p/cutadapt/
Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: cutadapt (RRID:SCR_011841) Copy
Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data.
Proper citation: Explicet (RRID:SCR_011937) Copy
An online toolbox for metagenomic data visualization.
Proper citation: MetaSee (RRID:SCR_011938) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
http://metavelvet.dna.bio.keio.ac.jp/
Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.
Proper citation: MetaVelvet (RRID:SCR_011915) Copy
http://swes.cals.arizona.edu/maier_lab/kartchner/documentation/index.php/home/docs/newbler
A software package for de novo DNA sequence assembly.
Proper citation: Newbler (RRID:SCR_011916) Copy
An open cloud company with performance Cloud Servers that offer 100% SSD storage & 10Gb Ethernet networking for your demanding applications.
Proper citation: Rackspace (RRID:SCR_011875) Copy
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