DADA2pipe: DADA2 pipeline function

In Djeppschmidt/SequenceSOP:

Description

This function implements the DADA2 sequence QC and annotation pipeline for amplicon sequence libraries. Requires a directory of fastq files that are named with _R1_001.fastq.gz or _R2_001.fastq.gz, formatted with searchable sample IDs incorporated into the file names. Depends on stringr and DADA2. Returns a phyloseq object with metadata.

Usage

DADA2pipe(
  in.dir,
  ref,
  ID,
  truncLen = c(200, 150),
  trimLeft = c(18, 19),
  maxN = 0,
  maxEE = c(2, 2),
  truncQ = 2,
  rm.phix = TRUE,
  compress = TRUE,
  multithread = TRUE
)

Arguments

in.dir	directory path to fastq files
ref	directory path to reference for taxomony annotation
ID	string to search file names for sample ID values
truncLen	where to truncate sequence forward and reverse reads. Default value is c(200, 150). See DADA2 documentation
trimLeft	removes bases from left, used to remove primers left over. Default value is c(18, 19). See DADA2 documentation
maxN	sets maximum number of N values in sequences that are retained. Default value is 0. See DADA2 documentation
maxEE	sets the maximum number of expected errors for each read. Default value is c(2,2). See DADA2 documentation
truncQ	paramter to tune sequence truncation. Default is 2. See DADA2 documentation
rm.phix	logical to remove PhiX. Default is TRUE. See DADA2 documentation
compress	logical. Default is TRUE. See DADA2 documentation
multithread	logical. Default is TRUE. See DADA2 documentation
metadf	metadata for sequence annotation

Examples

DAD2Apipe()

Djeppschmidt/SequenceSOP documentation built on Dec. 17, 2021, 5:27 p.m.