OPTIONS

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]

DESCRIPTION

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.

OPTIONS

-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

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)

AUTHOR

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.