This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-shortread
and update with:
conda update bioconductor-shortread
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-shortread.