bioconductor-shortread

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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.

Home http://bioconductor.org/packages/3.6/bioc/html/ShortRead.html
Versions 1.28.0, 1.32.0, 1.34.2, 1.36.0
License Artistic-2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-shortread

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-shortread

and update with:

conda update bioconductor-shortread

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-shortread.