Inctyper
Detection of Plasmid Inc types in assembly contigs.
About
Inctyper is an in-house tool that uses the PlasmidFinder database and BLAST to identify the contigs containing an Inc reference gene. The genus assignment from Speciator is used to select which PlasmidFinder library to search and a threshold of >=90% identity with E-value <1e-35 is used to gather matches. If you use the output of this tool in a publication, please cite Carattoli et al, 2014.
If a contig contains more than one Inc reference gene, then a composite type is reported with the Inc family codes separated by a double dash: '--' (e.g. IncY--Inc18 ).
Results in Genome Report
In the Inctyper section of the Genome Report, individual contigs are indicated by a background zebra striping. The Inc type and corresponding reference gene matches with percent identity and coverage are given for each contig. When AMR predictions are available, resistant genes found in Inc-containing contigs are also reported in the Inctyper section of the report.
Contig Inc type
Contig AMR genes
Match ID
% Identity
% Coverage
Results in Table
The identified Inc types are displayed in the "Typing" table as a comma-separated list.
Code Repository
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