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Swarm v3: towards tera-scale amplicon clustering.

Frédéric Mahé^1,2, Lucas Czech^3,4, Alexandros Stamatakis^3,5

¹UMR PHIM, CIRAD, Montpellier, France.

Bioinformatics (Oxford, England)

|July 10, 2021

Summary

The updated swarm v3 software offers faster and more efficient amplicon clustering for large datasets. This open-source program generates precise molecular operational taxonomic units (OTUs) without arbitrary thresholds.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The previous version of swarm provided open-source amplicon clustering for fine-scale molecular operational taxonomic units (OTUs).
Contemporary biological datasets are rapidly increasing in size, posing challenges for existing computational tools.

Purpose of the Study:

To present swarm v3, an enhanced version of the swarm software.
To address the computational demands of large-scale amplicon sequencing datasets.

Main Methods:

Modernized C++ source code for improved performance.
Optimized CPU usage and multithreading capabilities.
Extensive testing for robustness and logical consistency.

Main Results:

Swarm v3 demonstrates a significant speed increase, over 7 times faster with default parameters.
Reduced memory footprint by up to 50% compared to previous versions.
Enhanced performance and efficiency for processing tera-byte scale datasets.

Conclusions:

Swarm v3 provides a robust and efficient solution for amplicon clustering.
The updated software is well-suited for analyzing large and complex biological datasets.
Open-source availability facilitates widespread adoption and further development.