v1.3

v1.3 - [08/02/24]

• Rename --subsampling_off to --skip_subsampling
• Remove --brackendb parameter as redundant. Bracken will now use the database location specified with --krakendb.
• Update spoligotype database file (January 2024)
• Update TB-profiler to version 5.0.1 and remove external database as this version has Zwyer lineages incorporated
• Remove SpoTyping and use spoligotyping results from TB-profiler instead
• Change %Mapped column header in read_stats_summary.csv to %TrimMapped so as to make clearer that the % of reads mapped is based on the number of trimmed reads
• Documentation updated