Cargando…

Swarm v2: highly-scalable and high-resolution amplicon clustering

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-lin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2015
Materias:	Biodiversity
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690345/ https://www.ncbi.nlm.nih.gov/pubmed/26713226 http://dx.doi.org/10.7717/peerj.1420

Ejemplares similares

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

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

VSEARCH: a versatile open source tool for metagenomics
por: Rognes, Torbjørn, et al.
Publicado: (2016)

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

Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data
por: Kraus, Diana, et al.
Publicado: (2019)

Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing
por: Moll, Julia, et al.
Publicado: (2022)

A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)—patterns of nucleotide misincorporation
por: D’Ercole, Jacopo, et al.
Publicado: (2021)

Sharing for science: high-resolution trophic interactions revealed rapidly by social media
por: Maritz, Robin A., et al.
Publicado: (2020)

Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil
por: Oliveira, Pablo Viana, et al.
Publicado: (2020)

Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons
por: Pochon, Xavier, et al.
Publicado: (2019)

Low resolution scans can provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for 3D shape analyses
por: Marcy, Ariel E., et al.
Publicado: (2018)

High-resolution modeling of thermal thresholds and environmental influences on coral bleaching for local and regional reef management
por: Kumagai, Naoki H., et al.
Publicado: (2018)

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass
por: Phair, Nikki Leanne, et al.
Publicado: (2019)

Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections
por: Amiri, Navolle, et al.
Publicado: (2023)

Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome
por: Gavriliuc, Stefan, et al.
Publicado: (2021)

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region
por: Hume, Benjamin C.C., et al.
Publicado: (2018)

Limited influence of marine sediment lyophilization on prokaryotic community structure assessed via amplicon sequencing: an example from environmentally contrasted sediment layers in Toulon harbor (France)
por: Misson, Benjamin, et al.
Publicado: (2021)

Allopatric speciation is more prevalent than parapatric ecological divergence in a recent high-Andean diversification (Linochilus: Asteraceae)
por: Vargas, Oscar M., et al.
Publicado: (2023)

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts
por: Hui, Min, et al.
Publicado: (2022)

Raritas: a program for counting high diversity categorical data with highly unequal abundances
por: Lazarus, David B., et al.
Publicado: (2018)

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)

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
por: Leray, Matthieu, et al.
Publicado: (2015)

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
por: Ritter, Camila D., et al.
Publicado: (2018)

Highly divergent mussel lineages in isolated Indonesian marine lakes
por: Becking, Leontine E., et al.
Publicado: (2016)

Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic
por: Chaabane, Amira, et al.
Publicado: (2016)

High microphone signal-to-noise ratio enhances acoustic sampling of wildlife
por: Darras, Kevin F.A., et al.
Publicado: (2020)

Ontogeny of highly variable ceratitid ammonoids from the Anisian (Middle Triassic)
por: Bischof, Eva Alexandra, et al.
Publicado: (2021)

Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution
por: Bao, Riyue, et al.
Publicado: (2020)

High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis
por: Arocha-Garza, Hector Fernando, et al.
Publicado: (2017)

Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy
por: Kersten, Oliver, et al.
Publicado: (2019)

Cascading effects of a highly specialized beech-aphid–fungus interaction on forest regeneration
por: Cook-Patton, Susan C., et al.
Publicado: (2014)

Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
por: Reczuga, Monika K., et al.
Publicado: (2020)

Molecular diversity and distribution of marine fungi across 130 European environmental samples
por: Richards, Thomas A., et al.
Publicado: (2015)

High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt
por: Arriaga-Jiménez, Alfonsina, et al.
Publicado: (2018)

The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast
por: Govindarajan, Annette F., et al.
Publicado: (2019)

Unveiling the evolutionary relationships and the high cryptic diversity in Andean rainfrogs (Craugastoridae: Pristimantis myersi group)
por: Franco-Mena, Daniela, et al.
Publicado: (2023)

A Pan-Amazonian species delimitation: high species diversity within the genus Amazophrynella (Anura: Bufonidae)
por: Rojas, Rommel R., et al.
Publicado: (2018)

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
por: Winker, Kevin, et al.
Publicado: (2018)

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing
por: Hu, Zongfu, et al.
Publicado: (2018)

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
por: Wangensteen, Owen S., et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_3l6ugf87bn3dv96ej4ss2uabfu