decontaminate: Remove contaminant reads from a fastq file

In wilkox/fqdecontamr: Remove contaminant reads from fastq files

Description

Remove contaminant reads from a fastq file

Usage

decontaminate(fastq_file, decontam_file, index_dir, out_file,
  threads = 1)

Arguments

fastq_file	Path to the fastq file to be filtered. Can be in '.gz' compressed format
decontam_file	Path to decontam output, in .xlsx format
index_dir	Directory in which to store downloaded genomes and bowtie2 indices
out_file	Path to which the filtered fastq should be written
threads	How many threads should bowtie2 use when aligning (default 1)

Value

Returns a [tibble][tibble::tibble-package] of reads that have been removed and their taxonomic assignments

wilkox/fqdecontamr documentation built on Aug. 18, 2019, 4:36 a.m.