parse_swarms: Parse SWARM files

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Parse SWARM files

Description

This function reads the results of SWARM clustering (*.swarms file).

Usage

parse_swarms(x, otu_delimiter = " ")

Arguments

x	Input file name (usually with "swarm" extension)
otu_delimiter	Character string delimiting sequence IDs within a file line (default, whitespace)

Details

SWARM is a single-linkage clustering method with iterative growth process and the use of sequence abundance values to delineate OTUs. SWARM properly delineates large OTUs (high recall), and can distinguish OTUs with as little as two differences between their centers (high precision).

Value

data frame with two columns: OTU name and sequences names that belongs to this OTU.

See Also

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2015) Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 3:e1420 doi: 10.7717/peerj.1420 https://github.com/torognes/swarm https://github.com/frederic-mahe/swarm/wiki/Fred's-metabarcoding-pipeline

Examples

parse_swarms("tst_1f.swarms")

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.