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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
https://github.com/MikkelSchubert/adapterremoval
Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.
Proper citation: AdapterRemoval (RRID:SCR_011834) 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://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) 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
A general-purpose full virtualizer for x86 and AMD64/Intel64 hardware, targeted at server, desktop and embedded use.
Proper citation: VirtualBox (RRID:SCR_011876) Copy
http://omics.informatics.indiana.edu/GeneStitch/
Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.
Proper citation: GeneStitch (RRID:SCR_011910) Copy
Software that virtualizes computing, from the data center to the cloud to mobile devices, to help customers be more agile, responsive, and profitable.
Proper citation: VMware (RRID:SCR_011878) Copy
http://cs.stanford.edu/group/genovo/
Software for a novel de novo sequence assembler that discovers likely sequence reconstructions under the model.
Proper citation: Genovo (RRID:SCR_011911) Copy
A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.
Proper citation: METAREP (RRID:SCR_011926) Copy
A cloud-based platform to support genomics at your organization.
Proper citation: DNAnexus (RRID:SCR_011884) Copy
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