report: Example Complete Report after the following steps.
Blast data from attached blastdata table
SRST2 data from attached srst2data table
Description
read_blast Import the blast file, add column names
blast_parser Parse imported file
amr_positives Detect AMR positive plasmids
read_srst2 Import SRST2 file
combine_results Combine SRST2 and Blast
zetner_score Add Sureness value
amr_presence Add detected AMR to report
order_report Arrange report
Format
Dataframe.Source
Strains graciously provided by the authors of the following papers:
Complete Genome and Plasmid Sequences of Three Canadian Isolates of
Salmonella enterica subsp. enterica Serovar Heidelberg from Human
and Food Sources. 2016 Labbe et al.
PMID: 26769926 Complete Sequence of Four Multidrug-Resistant MOBQ1 Plasmids Harboring
blaGES-5 Isolated from Escherichia coli and Serratia marcescens
Persisting in a Hospital in Canada. 2015 Boyd et al.
PMID: 25545311 Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with
blaNDM-1 Arrives in North America. 2016 Mataseje et al.
PMID: 26824951