removeChimeraMulti: removeChimeraMulti

In derele/MultiAmplicon: Metabarcoding and microbiome analysis using multiple amplicons

removeChimeraMulti

Description

Remove chimeric sequencing read pairs from a MultiAmplicon object.

Usage

removeChimeraMulti(MA, mc.cores = getOption("mc.cores", 1L), ...)

Arguments

MA	A MultiAmplicon-class object preprocessed to have the sequenceTable slot filled.
mc.cores	integer number of cores to use for parallelization accross different amplicons.
...	passed on to removeBimeraDenovo. All arguments to the function can be given as a vector of the same length as the number of primer pairs in the MultiAmplicon object, allowing to specify different parameters for each amplicon. If a shorter vector is given it will be recycled to match the number of amplicons.

Details

This is a wrapper for the removeBimeraDenovo function of dada2. It works on an MultiAmplicon-class object with the sequenceTable slot filled. Use dadaMulti, derepMulti, mergeMulti and makeSequenceTableMulti on a amplicon sorted (see sortAmplicons) MultiAmplicon-class object to preprocess your multi-marker data to this point.

Value

a MultiAmplicon-class object with the sequenceTableNoChime filled

Author(s)

Emanuel Heitlinger

derele/MultiAmplicon documentation built on Dec. 11, 2024, 12:09 p.m.