Swarm v2: highly-scalable and high-resolution amplicon clustering
- Published
- Accepted
- Subject Areas
- Biodiversity, Bioinformatics, Environmental Sciences, Microbiology, Molecular Biology
- Keywords
- environmental diversity, barcoding, molecular operational taxonomic units
- Copyright
- © 2015 Mahé et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ PrePrints 3:e1222v2 https://doi.org/10.7287/peerj.preprints.1222v2
Abstract
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 that 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.
Author Comment
This new version includes a HTML supplement presenting the code used to run the analyzes.
Supplemental Information
Supplementary File
Data and code snippets used to produce the results presented in the manuscript