Swarm v3: towards tera-scale amplicon clustering

Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

(2020) Luciana Santoferrara et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean

(2019) Caterina R. Giner et al.   ISME Journal

The State of Software for Evolutionary Biology

(2018) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniEuk : Time to Speak a Common Language in Protistology!

(2017) Cédric Berney et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

(2015) Frédéric Mahé et al.   PeerJ

Best Practices for Scientific Computing

(2014) Greg Wilson et al.   PLOS BIOLOGY

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

(2014) Frédéric Mahé et al.   PeerJ

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS