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Plasmid Profiler (version 0.1.6.1)

What it does

Heatmap display of plasmid content in WGS data

This program parses plasmids identified through SRST2 and BLAST, scores them based on a combined measure of maximized coverage and minimized sequence divergence, and produces visualizations along with tabular results. Best used on results from the workflow "P2 - Plasmid Profiler: SRST2 and BLAST"

Usage

BLAST TSV file name:
  • Tab separated value table of BLAST results from querying plasmidfinder database with AMR sequences against SRST2 identified plasmids
SRST2 TSV file name:
  • Tab separated value table of SRST2 results from querying WGS reads against plasmid database
Sureness cut off:
  • Sureness is the difference between normalized sequence coverage and divergence. It is a unique measure per dataset that informs the user as to the likelihood the identified plasmid is present in their sample. A value of 0.75 is recommended for a first pass with plasmids scoring above 0.95 to be considered as present in the WGS data.
Plasmid length cut off:
  • Remove all plasmid sequences below this length from results (eg. 10000)
Percent coverage cut off:
  • Plasmids with read coverage below this percentage will be excluded from the results (eg. 75)
Plot title:
  • Custom plot title for heatmap
Anonymize plasmids and sample names:
  • Hide identifiers in final image and replace with "Plasmid #" and "Sample #"
Combine very closely related incompatibility groups:
  • Collapse subtypes of incompatibility groups. (eg. FII(S) and FII(K) collapsed to FII)
Acknowledgments

Plasmid Profiler Author: Adrian Zetner

Galaxy tool author: Jen Cabral