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 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 ).

Genome Report

In the Inctyper section of the genome report individual contigs are indicated by the 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 reported in the Inctyper section of the Genome Report.

Collection View

The identified Inc types are displayed in the "Typing" table as a comma-separated list and are available for download in the associated CSV.

Downloads

The full Inctyper download includes the following fields and has one line per matched reference gene:

• Genome ID - The internal unique genome identifier.

• Genome Name - The name of the assembly.

• Contig - The name of the contig with the Inc/Rep match as according to the original BLAST file.

• Match ID - The name of the matched representative gene.

• Group Inc Match - The Inc/Rep group of the match.

• Percent Identity - The percent identity of the two matches as calculated by BLAST.

• Match Coverage - the percentage coverage of the reference gene that has been matched.

• Contig Start - start location of the BLAST match in the query contig

• Contig End - end location of the BLAST match in the query contig

• Reference Start - Start location of the BLAST match in the reference Inc/Rep gene.

• Reference End - End location of the BLAST match in the reference Inc/Rep gene.

How to cite

Inctyper is based on the plasmidfinder library:

Carattoli A, Zankari E, García-Fernández A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895-3903. doi:10.1128/AAC.02412-14

The software is available under an OSS licence from https://github.com/pathogenwatch-oss/inctyper