scores_vs_expected(1) parse scores from SRST(v2)


scores_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]


SRST2 - 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
--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)


Harriet Dashnow ([email protected]), Kathryn Holt ([email protected])

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.