Cargando…

VSEARCH: a versatile open source tool for metagenomics

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 pub...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rognes, Torbjørn, Flouri, Tomáš, Nichols, Ben, Quince, Christopher, Mahé, Frédéric
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2016
Materias:	Biodiversity
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075697/ https://www.ncbi.nlm.nih.gov/pubmed/27781170 http://dx.doi.org/10.7717/peerj.2584

Ejemplares similares

Swarm: robust and fast clustering method for amplicon-based studies
por: Mahé, Frédéric, et al.
Publicado: (2014)

Swarm v2: highly-scalable and high-resolution amplicon clustering
por: Mahé, Frédéric, et al.
Publicado: (2015)

Comparison of three clustering approaches for detecting novel environmental microbial diversity
por: Forster, Dominik, et al.
Publicado: (2016)

Swarm v3: towards tera-scale amplicon clustering
por: Mahé, Frédéric, et al.
Publicado: (2021)

DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
por: Antich, Adrià, et al.
Publicado: (2022)

Metagenomic and satellite analyses of red snow in the Russian Arctic
por: Hisakawa, Nao, et al.
Publicado: (2015)

Evaluation of ddRADseq for reduced representation metagenome sequencing
por: Liu, Michael Y., et al.
Publicado: (2017)

Bioreactor virome metagenomics sequencing using DNA spike-ins
por: Cremers, Geert, et al.
Publicado: (2018)

Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes
por: Verstraete, Brecht, et al.
Publicado: (2023)

Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data
por: Holmes, Iris, et al.
Publicado: (2018)

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem
por: Ghosh, Anwesha, et al.
Publicado: (2022)

Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758)
por: Cuartas, Jaison H., et al.
Publicado: (2018)

Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole
por: Zhang, Hongxi, et al.
Publicado: (2023)

Open-Source Sequence Clustering Methods Improve the State Of the Art
por: Kopylova, Evguenia, et al.
Publicado: (2016)

Marine aquaculture as a source of propagules of invasive fouling species
por: Lins, Daniel M., et al.
Publicado: (2023)

Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species
por: Jaskuła, Radomir, et al.
Publicado: (2019)

Functional macrophyte trait variation as a response to the source of inorganic carbon acquisition
por: Chmara, Rafał, et al.
Publicado: (2021)

Limited effects of source population identity and number on seagrass transplant performance
por: Novak, Alyssa B., et al.
Publicado: (2017)

Inconsistencies among secondary sources of Chukar Partridge (Alectoris chukar) introductions to the United States
por: Moulton, Michael P., et al.
Publicado: (2015)

Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan
por: Lin, Tzong-Han, et al.
Publicado: (2023)

Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae)
por: Engelbrecht, Hanlie M., et al.
Publicado: (2021)

Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation
por: Jo, Seung-Woo, et al.
Publicado: (2020)

Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework
por: Butti, Mariella, et al.
Publicado: (2022)

Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment
por: Yoshioka, Akira, et al.
Publicado: (2020)

Quiz-style online training tool helps to learn birdsong identification and support citizen science
por: Ogawa, Yui, et al.
Publicado: (2023)

From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion
por: Cuezzo, Maria Gabriela, et al.
Publicado: (2018)

Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
por: DiBattista, Joseph D., et al.
Publicado: (2019)

New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes
por: Janik, Paulina, et al.
Publicado: (2020)

Mitochondrial sequence data reveal population structure within Pustulosa pustulosa
por: Rodriguez, David, et al.
Publicado: (2023)

Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines
por: Bogdan, Vlastimil, et al.
Publicado: (2016)

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics
por: Goll, Johannes, et al.
Publicado: (2010)

Consequences for selected high-elevation butterflies and moths from the spread of Pinus mugo into the alpine zone in the High Sudetes Mountains
por: Bílá, Karolína, et al.
Publicado: (2016)

Reduced metagenome sequencing for strain-resolution taxonomic profiles
por: Snipen, Lars, et al.
Publicado: (2021)

Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea
por: Bertucci, Frédéric, et al.
Publicado: (2017)

Niche diversification of Mediterranean and southwestern Asian tortoises
por: Escoriza, Daniel, et al.
Publicado: (2022)

First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species
por: Popoola, Michael Olaoluwa, et al.
Publicado: (2022)

Spatial patterns of bat diversity overlap with woodpecker abundance
por: Kotowska, Dorota, et al.
Publicado: (2020)

Refining the marine reptile turnover at the Early–Middle Jurassic transition
por: Fischer, Valentin, et al.
Publicado: (2021)

Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects
por: Elbrecht, Vasco, et al.
Publicado: (2016)

A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity
por: Stocker, Michelle R., et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_6b00g2l3p68u49k3qnal56a5ti