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http://www.utoronto.ca/

Public research university in Toronto, Ontario, Canada, located on the grounds that surround Queen's Park.

Proper citation: University of Toronto; Ontario; Canada (RRID:SCR_011733) Copy   

•   Source: SciCrunch Registry

http://www.unitn.it/en

Italian university located in Trento and nearby Rovereto. It has been able to achieve considerable results in didactics, research, and international relations according to CENSIS and the Italian Ministry of Education.

Proper citation: University of Trento; Trento; Italy (RRID:SCR_011734) Copy   

•   Source: SciCrunch Registry

http://www.waikato.ac.nz/

Waikato University, is a comprehensive university in Hamilton, New Zealand. The university was established in 1964, and has an additional campus located in Tauranga.

Proper citation: University of Waikato; Hamilton; New Zealand (RRID:SCR_011745) Copy   

•   Source: SciCrunch Registry

http://en.uw.edu.pl/

University was established in 1816 and is the largest university in Poland. One of the top Polish universities.

Proper citation: University of Warsaw; Warsaw; Poland (RRID:SCR_011747) Copy   

•   Source: SciCrunch Registry

http://www2.warwick.ac.uk/

Public research university on the outskirts of Coventry between the West Midlands and Warwickshire, England. It was founded in 1965 as part of a government initiative to expand higher education.

Proper citation: University of Warwick; Coventry; United Kingdom (RRID:SCR_011748) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.utk.edu/

Public research university in Knoxville, Tennessee.

Proper citation: University of Tennessee Knoxville; Tennessee; USA (RRID:SCR_011714) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.uthscsa.edu/

The University of Texas Health Science Center at San Antonio serves San Antonio and the 50,000 square-mile area of South Texas. It extends to campuses in the metropolitan border communities of Laredo and the Rio Grande Valley. More than 3,000 students a year train in an environment that involves more than 100 affiliated hospitals, clinics and health care facilities in South Texas.

Proper citation: University of Texas Health Science Center at San Antonio; Texas; USA (RRID:SCR_011722) Copy   

•   Source: SciCrunch Registry

http://www.utsouthwestern.edu/

Public academic health science center in Dallas, Texas.

Proper citation: University of Texas Southwestern Medical Center; Texas; USA (RRID:SCR_011724) Copy   

•   Source: SciCrunch Registry

http://www.explicet.org/

Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data.

Proper citation: Explicet (RRID:SCR_011937) Copy   

•   Source: SciCrunch Registry

http://www.metasee.org/

An online toolbox for metagenomic data visualization.

Proper citation: MetaSee (RRID:SCR_011938) Copy   

•   Source: SciCrunch Registry

http://genopole.pasteur.fr/SynTView/

An interactive multi-view genome browser for next-generation comparative microorganism genomics.

Proper citation: SynTView (RRID:SCR_011939) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php

A Next-Generation Sequencing Simulator for Metagenomics.

Proper citation: NeSSM (RRID:SCR_011941) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry