prep_illSE: standard preprocessor for SINGLE-END Illumina reads in BiMiCo...

In peterolah001/BiMiCo: Biomap Microbiome Core methods

standard preprocessor for SINGLE-END Illumina reads in BiMiCo pipeline

Description

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

Usage

prep_illSE(readfiles, outdir, file_suffix = ".fastq", mtthread = F,
  trim_read_length = 0, trim5end = 0)

Arguments

readfiles	(Required) Path to single-end Illumina demultiplexed fastq files
outdir	(Required) String specifying output directory for processed files; will be created as subdirectory of input dir.
file_suffix	(Optional) Please specify if input files have special suffixes other than ".fastq", e.g. "_filt.hf.fq". Default=".fastq"
mtthread	(Optional) Boolean, enables multithreading (not recommended in Rstudio). Default=F
trim_read_length	(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_illSE()

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