chimera_detection_vs: Detect for chimera taxa using vsearch

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Detect for chimera taxa using vsearch

Description

Use the VSEARCH software.

Usage

chimera_detection_vs(
  seq2search,
  nb_seq,
  vsearchpath = "vsearch",
  abskew = 2,
  min_seq_length = 100,
  vsearch_args = "--fasta_width 0",
  keep_temporary_files = FALSE
)

Arguments

seq2search	(required) a list of DNA sequences coercible by function Biostrings::DNAStringSet()
nb_seq	(required) a numeric vector giving the number of sequences for each DNA sequences
vsearchpath	(default: vsearch) path to vsearch
abskew	(int, default 2) The abundance skew is used to distinguish in a three way alignment which sequence is the chimera and which are the parents. The assumption is that chimeras appear later in the PCR amplification process and are therefore less abundant than their parents. The default value is 2.0, which means that the parents should be at least 2 times more abundant than their chimera. Any positive value equal or greater than 1.0 can be used.
min_seq_length	(int, default 100)) Minimum length of sequences to be part of the analysis
vsearch_args	(default "–fasta_width 0") A list of other args for vsearch command
keep_temporary_files	(logical, default: FALSE) Do we keep temporary files ? non_chimeras.fasta chimeras.fasta borderline.fasta

Details

This function is mainly a wrapper of the work of others. Please make vsearch.

Value

A list of 3 including non-chimera taxa (⁠$non_chimera⁠), chimera taxa (⁠$chimera⁠) and bordeline taxa (⁠$borderline⁠)

Author(s)

Adrien Taudière

See Also

chimera_removal_vs(), dada2::removeBimeraDenovo()

Examples

chimera_detection_vs(
  seq2search = data_fungi@refseq,
  nb_seq = taxa_sums(data_fungi)
)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.