README.md

In wilkox/fqdecontamr: Remove contaminant reads from fastq files

fqdecontamr filters fastq files to remove reads identified as potential contaminants by decontam.

Installation

You can install the development version of fqdecontamr from GitHub with:

devtools::install_github("wilkox/fqdecontamr")

How to use

fqdecontamr requires two input files:

• The decontam output, in the form of a Microsoft Excel spreadsheet (*.xlsx)
• The fastq file you want to filter (gzip compressed files are accepted)

The main function provided by fqdecontamr is called decontaminate(). It takes as arguments the paths to the two input files listed above ( decontam_file and fastq_file), a third argument index_dir specifying a directory in which to cache downloaded genomes and bowtie2 index files, and a fourth argument out_file specifying where to write the filtered fastq file. decontaminate() returns a tibble listing the reads that were removed and the contaminant species to which they aligned.

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