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/swarm.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Mahe F 

PROVIDER: S-EPMC8696092 | biostudies-literature |

REPOSITORIES: biostudies-literature