Note: these pipelines were developed for the CRyPTIC project which studies M. tuberculosis, but in principle can be used on any bacteria.

Clockwork takes fastq input and outputs standard VCF files as output

Please see the clockwork wiki page for documentation.

If you use Clockwork for variant calling please cite the following paper, where it was introduced and benchmarked:

"Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes". Hunt et al. Genome Biol. 2022 Jul 5;23(1):147. doi: 10.1186/s13059-022-02714-x.

Whilst Minos is the novel part of the Clockwork variant calling pipeline, it uses several other tools. Please also cite:

• Minimap2 https://doi.org/10.1093/bioinformatics/bty191
• SAMtools https://doi.org/10.1093/gigascience/giab008
• Cortex https://doi.org/10.1038/ng.1028
• Trimmomatic: https://doi.org/10.1093/bioinformatics/btu170