期刊
PEERJ
卷 3, 期 -, 页码 -出版社
PEERJ INC
DOI: 10.7717/peerj.1420
关键词
Environmental diversity; Barcoding; Molecular operational taxonomic units
资金
- Deutsche Forschungsgemeinschaft [DU1319/1-1]
- EPSRC Career Acceleration Fellowship [EP/H003851/1]
- EU EraNet BiodivErsA program BioMarKs [2008-6530]
- French government Investissements d'Avenir project OCEANOMICS [ANR-11-BTBR-0008]
- EU FP7 program MicroB3 [287589]
- Engineering and Physical Sciences Research Council [EP/H003851/1] Funding Source: researchfish
- EPSRC [EP/H003851/1] Funding Source: UKRI
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-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
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