gene splitted into two contigs

Question

[elina2410]

Hello, I need help in interpreting abricate (vfdb) result. Based on the 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?

How would you interpret these results?

Thank you in advance.

Answer 1

[Max Sikolenko]

Yes, I think you are right. Looks like the two contigs have an edge “inside” of the hilA gene.

To check this guess, I probably would join the two contigs, then annotate them (e.g. using prokka), then check if prokka regards the junction as an hilA gene. Even if junction contains an unrecognized ORF, you can blast its sequence and check if it is similar to hilA.

To join the contigs correctly, you can investigate their “sticky ends” using the combinator-FQ tool.