Entering edit mode
4.5 years ago
chronotope
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10
Hi everyone! I have the task to co-assemble and bin (and then annotate / analyse function) a low-coverage single genome from 3 deeply sequenced libraries of 3 similar low diversity systems (<50 OTUs) (host-symbiont).
It seems wrong to just do megahit in1 in2, but I couldn't find any other visibly necessary options in the megahit option list, so I thought I'd ask for expert advice - what I should look out for, given my input above, and what kind of options might be useful to maximize the efficiency without breaking specificity and generating chimeras.
I would also be happy to be pointed at practical tutorials on assembling and recovering the genome in my specific case, I just couldn't find one (after a quick search)
Cheers! A
Is it de-novo or you have a good reference? If you have a reference I would map the reads to it, grab all the reads that map and assemble. A low coverage genome might get lost ("corrected") even in low diversity metagenome
16S phylogeny reconstruction gives me a new family level clade, so I am afraid any available related genome would only complicate things. So yeah, de novo
Can't think of another solution but combine all reads and assemble (would use meta-SPAdes though) and bin with metabat2.
Thank you, will look into that : ) I was wondering whether there are any specific flags that I shouldn't miss on in such a case, but I guess there isn't much