Duplicate contigs

[MonicaSteffi]

Dear Developer,

I am using spades to assemble my viral genome with the default setting. In total, I got 5 contigs, two of which are exactly the same. I did compare using blast pairwise alignment and I got 100% identity with 100% query coverage. And also, Blastn results gave the same hit.

Why do spades generate two contigs exactly the same sequences? How do I interpret this?

Thank you in advance

[asl]

Tagging @Dmitry-Antipov

[Dmitry-Antipov]

Hi
If you were using --metaviral option, likely it is a known minor bug. See this thread for more detailed discussion and suggestions. #1079