Using different assemblies to create a whole genome (bacteria)

Question

[keith.t.yamada]

Hello all,

I have 3 strains of bacteria, one wildtype and 2 mutants derived from the wildtype. I sequenced all 3 genomes with MiSeq 2x300bp. All of the genomes are still in contigs. I would like to align these contigs to see if some overlap in an attempt to fill in gaps and make a more complete genome or at least to see if the mutants have any large deletions. Does anyone know of a program that can do this kind of alignment?

(PS. I know this won't work if it ends up being that the mutants are severely different than the wildtype, but I think they should be fairly similar, i.e. just point mutations)

Thank you in advance!

[GenoMax]

Have you tried to take all of the data together and try to do an assembly. If you only expect point mutations in the mutants then you may be able to put a reasonable assembly together. You can then go back and map your individual reads to see where the discrepancies are.

Take a look at Mauve which will give you an idea of how the three assemblies you currently have related to each other.

Answer 1

[h.mon]

There are several assembly reconciliation tools, they may work for your use case. See this recent review for a good list of tools and their features: A comparative evaluation of genome assembly reconciliation tools.

If there is a close relative with a complete, closed genome assembly available, you could map all your assemblies and / or raw sequencing reads to this reference using minimap2 / bwa mem and visualize the alignment with IGV.