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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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gene splitted into two contigs? #202

Open elina2410 opened 9 months ago

elina2410 commented 9 months ago

Hello, I need help in interpreting abricate (vfdb) result. Based on result below can I assume that there is hilA gene in the analyzed strain? I mean if I can sum coverage results for these fragments and assume that I have 100% coverage for hilA gene?

obraz

How would you interpret these results?

Thank you in advance.

ammaraziz commented 5 months ago

Yes that's correct, you have hilA gene. Looks like during denovo assembly (spades?) the gene was split in half across two contigs.

Post denovo you can perform scaffolding ( I like ragtag) which should merge the two contigs.

Assumptions are that you have only one copy of hilA, this is an isolate with one strain and you have correctly performed denovo.