Swarm v2: highly-scalable and high-resolution amplicon clustering (Q40162665)

18 September 2017

Swarm v2: highly-scalable and high-resolution amplicon clustering (English)

1 reference

18 September 2017

1 reference

Torbjørn Rognes

2

0 references

Christopher Quince

object named as

Christopher Quince

series ordinal

3

0 references

Micah Dunthorn

series ordinal

5

object named as

Micah Dunthorn

1 reference

18 September 2017

4

Colomban de Vargas

1 reference

18 September 2017

1

Frédéric Mahé

1 reference

PMCID

4690345

18 September 2017

language of work or name

1 reference

10 December 2015

1 reference

18 September 2017

1 reference

18 September 2017

3

1 reference

18 September 2017

e1420

1 reference

Creative Commons Attribution 4.0 International

18 September 2017

start time

10 December 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Ocean plankton. Determinants of community structure in the global plankton interactome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany).

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

The Earth Microbiome project: successes and aspirations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Patterns of rare and abundant marine microbial eukaryotes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

CD-HIT: accelerated for clustering the next-generation sequencing data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Search and clustering orders of magnitude faster than BLAST

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

QIIME allows analysis of high-throughput community sequencing data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Defining DNA-based operational taxonomic units for microbial-eukaryote ecology

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Swarm: robust and fast clustering method for amplicon-based studies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4690345

20 August 2018

Identifiers

DOI

10.7717/PEERJ.1420

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

4690345