I have bins from metagenomes generated with metabat2 on bitbucket/berkleylab/scr which are predicted as viral by MARVEL. MARVEL suggests to merge contigs with overlapping ends with PHRAP but the documentation on the tool doesn't seem great.

As it appears to be an assembler would it be okay to use another assembler? For example one of my bins has 4 contigs ~1000-5000bp in length. 3 of these seem to overlap with each other enitirely.

I found a tool MeGAMerge on github which might work. Has anyone used this?


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