SWARM3 Module

This module use the swarm v3 software to create an OTU table.

Updates

swarm 3.0 introduces:

• a much faster default algorithm
• a reduced memory footprint
• strict dereplication of input sequences is now mandatory,
• seeds outputs results sorted by decreasing abundance, and then by alphabetical order of sequence labels.
• the representative sequence is the most abundant in the cluster

Module interactions

Main inputs

• Sequence files: Select all the FASTA files that you want to merge to perform the clustering.
• OTUs table: The OTUs table in tsv format. each line is a cluster and each column a sample. The numbers in the matrix is the number of reads for the cluster in the sample.
• Sort the samples: If checked, sort the samples in the matrix using the csv file entered in the following input.
• Most abundant reads: Each centroid sequence for clusters in FASTA format. The first sequence represent the 0th cluster centroid, the second sequence, the 1th cluster centroid, ...
• All reads: A file containing all the reads with their cluster assignment.

Options

• d value: The maximum distance between two reads in the same cluster. If d=1, the fastidious option is automatically set (see swarm github).

References

• Swarm github: https://github.com/torognes/swarm
• Swarm publication: https://peerj.com/articles/593/
• Swarm v3 publication: https://academic.oup.com/bioinformatics/article/38/1/267/6318385