FastQ Screen v0.16.0

Added functionality to process long sequence reads by using Minimap2 as the aligner.

We would like to thank Martin Pollard (Wellcome Sanger Institute, UK) for contributing this improvement.

FastQ Screen v0.15.3

Fixed filtering bug causing the final filtered FASTQ file to have the file extension .fastq when it should be .fastq.gz, since the file is actually gzipped.

FastQ Screen v0.15.2

Release notes for FastQ Screen v0.15.2 (26 January 2022)

Updated documentation

Provided details on the genomes downloaded with the
command --get_genomes for possible future reference.

FastQ Screen v0.15.1

Release notes for FastQ Screen v0.15.1 (11 January 2022)

Updated contact details.

FastQ Screen v0.15.0

Added remove_tags.pl in new Misc folder. This script removes FastQ Screen genome filter tags from read headers, which may be necessary for downstream analysis.

Downloading test genomes with wget now executed with --no-check-certificate parameter, to prevent downloading failures on some systems.

Release v0.14.1

Added --score_min L,0,-0.6 as a Bismark/Bowtie2 mapping
parameter to make FastQ Screen perform less stringent
mapping, which is more consistent with non-bisulfite
FastQ Screen mapping.

Added a GitHUb Actions YAML file for testing FastQ Screen.

Release v0.14.0

New --add_genome option.

Fixed bug causing FastQ Screen to run when aligner not present.

Release v0.13.0

Added --get_genomes option.
Updated documentation.

Released v0.12.2

GitHub issue #1: fastq_screen in --bisulfite mode now runs Bismark in…

Release v0.12.1 especially for Zenodo

F1000 required a ‘public registration’ for the project in order to obtain a DOI. This will be included in the Software availability section under ‘Archived source code as at time of publication’.