how to create a consensus sequence from different assemblies

Question

[andreapamela.aguilar]

I have files.fasta (some with multiple contigs) that are different versions of a plasmid reconstruction (we use Illumina to get the reads). How can I get a consensus sequence from them? Is there a program to create this consensus?

Answer 1

[Brian Bushnell]

BBTools has a program to make a consensus from alignments. It's helpfully called "consensus.sh". You can either align all the assemblies to one assembly and make a consensus from the sam file, or align all the reads to one assembly and make a consensus from that sam file. These are good approaches when the assemblies are quite similar (no major rearrangements). If there ARE major structural differences then I'm not sure a consensus is a good idea or the best way to go about it.

There are also, I'm sure, ways of doing this via multiple sequence alignments, but I've never personally used them.