long-reads

AMR detection in uncorrected long reads. Input is uncorrected/corrected nanopore sequenced reads.

See Docs

A possible approach

• Locate AMR genes.

• Fetch long reads.

• Consensus.

Output

• Sytenic block of ARGs, mutuations in those genes.

• Plasmid typing on reads associated with the ARGs.

• Plot options - Artemis looking output.

• Circularity of reads with detected AMR gene?

Previous & related tools:

• plasmid typing from long reads: andrewjpage/tiptoft

• Database of plasmid: plsdb

• Database of plasmid: itsmeludo/COMPASS

• Plasmid typing: aldertzomer/RFPlasmid

• Plasmid classifier: santirdnd/COPLA

• Plasmid detection + typing: MobSuite

Output libraries

• https://flanker.readthedocs.io/en/latest/
• https://github.com/gamcil/clinker
• https://cran.r-project.org/web/packages/gggenes/vignettes/introduction-to-gggenes.html