Question: Co-assembling a low-coverage genome from multiple libraries
gravatar for artiefinnigan
16 months ago by
artiefinnigan0 wrote:

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

metagenome assembly genome • 269 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by artiefinnigan0

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

ADD REPLYlink written 16 months ago by Asaf8.5k

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

ADD REPLYlink written 16 months ago by artiefinnigan0

Can't think of another solution but combine all reads and assemble (would use meta-SPAdes though) and bin with metabat2.

ADD REPLYlink written 16 months ago by Asaf8.5k

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

ADD REPLYlink written 16 months ago by artiefinnigan0
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