OPTIONSscores_vs_expected [-h] --scores SCORES [SCORES ...] --output OUTPUT [--mlst_delimiter MLST_DELIMITER] [--known_alleles KNOWN_ALLELES] [--known_STs KNOWN_STS] [--ST_definitions ST_DEFINITIONS] [--ignore_last] [--min_coverage MIN_COVERAGE] [--min_depth MIN_DEPTH] [--min_edge_depth MIN_EDGE_DEPTH]
DESCRIPTIONSRST2 - Short Read Sequence Typer (v2): Outputs score and gene summaries. Reference fasta must have been in format cluster#__gene__allele
Parses scores from SRST(v2) to produce a summary table of the top scoring allele for each locus/cluster for multiple samples. If a table of known/expected alleles are provided, this info is also included in the scores summary output.
- -h, --help
- show this help message and exit
- --scores SCORES [SCORES ...]
- One or more .scores files produced by srst2.py
- --output OUTPUT
- Prefix for output tables summarising the top scoring allele for each gene with more detailed score information, and ST table.
- --mlst_delimiter MLST_DELIMITER
- Character that separates locus symbol from allele number (e.g. "-")
- --known_alleles KNOWN_ALLELES
- File of known alleles for comparison (tab-delimited)
- --known_STs KNOWN_STS
- File of known STs for comparison (tab-delimited), must also provide ST definitions table (--mlst)
- --ST_definitions ST_DEFINITIONS
- Table of ST definitions
- Ignore last column of ST profiles table (e.g. sometimes an additional column is added to indicate clonal complex, which is not part of the ST definition).
- --min_coverage MIN_COVERAGE
- Percent coverage cutoff for gene reporting (default 90)
- --min_depth MIN_DEPTH
- Minimum mean depth to flag as dubious allele call (default 5)
- --min_edge_depth MIN_EDGE_DEPTH
- Minimum edge depth to flag as dubious allele call (default 2)