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VSEARCH: a versatile open source tool for metagenomics

Rognes, Torbjorn; Flouri, Tomas 1; Nichols, Ben; Quince, Christopher; Mahe, Frederic
1 Institut für Theoretische Informatik (ITI), Karlsruher Institut für Technologie (KIT)

Abstract:

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.
Methods. When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.
Results. VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. ... mehr


Volltext §
DOI: 10.5445/IR/1000062113
Originalveröffentlichung
DOI: 10.7717/peerj.2584
Scopus
Zitationen: 3774
Web of Science
Zitationen: 3634
Dimensions
Zitationen: 4619
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2016
Sprache Englisch
Identifikator ISSN: 2167-8359
urn:nbn:de:swb:90-621136
KITopen-ID: 1000062113
Erschienen in PeerJ
Verlag PeerJ
Band 4
Seiten Art.Nr.: e2584
Schlagwörter Clustering, Chimera detection, Searching, Masking, Shuffling, Parallellization, Metagenomics, Alignment, Sequences, Dereplication
Nachgewiesen in Web of Science
Dimensions
Scopus
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