Swarm v3: towards tera-scale amplicon clustering
Abstract
Motivation: Previously we presented swarm, an open-source amplicon clustering program that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes.Results: When compared to previous swarm versions, swarm v3 has modernized C ++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic.Availability: Source code and binaries are available at https://github.com/torognes/swarmSupplementary information: Supplementary data are available at Bioinformatics online.
| Origin | Publication funded by an institution |
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