Clockwork database

This database (clockwork) contains common sputum contaminants along with a selection of NTM genomes and H37Rv - as used in the Clockwork pipeline (https://github.com/iqbal-lab-org/clockwork). In addition, we added 17 high-quality M. tuberculosis genomes to this collection (from https://doi.org/10.1186/s13059-021-02474-0 - see mtb_gramtools_lineages.csv for the list of accessions). The database was downloaded using the download_tb_reference_files.pl script. The 17 MTB genomes were downloaded from https://doi.org/10.5281/zenodo.4147301. The db.tsv file contains a mapping from the sequence identifier to the category of that assembly - i.e. human, TB, Bacteria etc. The minimap2.db.acc2tax.tsv maps those sequences with known accession numbers to their taxonomic identifier.