[mira_talk] Denovo versus mappings assembly with Mira
- From: David Coil <coil.david@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 11 May 2013 14:02:03 -0700
Greetings all,
My questions is closer to biology than bioinformatics but I figured I'd
give it a shot here. So I've been using Mira to do a bunch of both de
novo and mapping assemblies recently. The mapping assembly output from
Mira is great for checking out SNPs etc.
But I'm wondering if the results of a mapping assembly (using the
-SB:abnc-yes flag) count as a "genome sequence". Basically you get one
big contig (the mapping) and then a number of small ones assembled from the
leftovers. But the big mapped contig has gaps even though it's called a
"contig". You'd have to break the contig on those gaps to say, submit the
genome to NCBI even though many of them are very small. One could of
course use the unpadded result, but then you may be joining things together
over large gaps that really should be considered separate contigs.
So it seems to me that mapping assemblies are great for answering
biological questions... but insufficient to say publish the genome sequence
of an isolate. Would people agree or disagree with that idea? Am I
thinking about the mapping assemblies incorrectly?
Thanks for any thoughts!
David Coil, PhD
Eisen Lab
UC Davis
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