prep_illPE: standard preprocessor for PAIRED-END Illumina reads in BiMiCo...

In peterolah001/BiMiCo: Biomap Microbiome Core methods

standard preprocessor for PAIRED-END Illumina reads in BiMiCo pipeline

Description

Convenience wrapper for DADA2 read processing functions. Given a directory of raw Illumina fastq files, performs platform-specific trimming and QC, writes reads to output directory.

Usage

prep_illPE(fwd_reads, rev_reads, rawext, filt_out, mtthread = F,
  trim_read_length_FWD = 0, trim_read_length_REV = 0, trim5end = 0)

Arguments

fwd_reads	(Required) Path to READ1 paired-end demultiplexed fastq files
rev_reads	(Required) Path to READ1 paired-end demultiplexed fastq files
rawext	(Required) READ1 fastq file precise extension, UNIQUE PART WITH READ NUMBER as string, e.g. "_1.fastq"
filt_out	(Required) String specifying path to write quality-filtered fastq files to (relative or absolute path).
mtthread	(Optional) Boolean, enables multithreading (not recommended in Rstudio). Default=F
trim_read_length_FWD	(Optional) max. length at which to truncate reads. Default = 0 (no truncating)
trim_read_length_REV	(Optional) max. length at which to truncate reads. Default = 0 (no truncating)
trim5end	(Optional) trim n reads from the start of reads (unidentified adapters, barcodes). Default=0 (no trimming)

Examples

prep_illPE()

peterolah001/BiMiCo documentation built on April 24, 2023, 3:35 a.m.