Question: Align two microbial genomes -- is mummer still the way to go?
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gravatar for Lina F
3.2 years ago by
Lina F190
Boston, MA
Lina F190 wrote:

Hi all,

I have assemblies of two microbial genomes from PacBio data (49 and 69 contigs each) and I'm trying to figure out how similar they are. The final genome size should be about 7.5 Mb.

I remembered the mummer tools from a project many years ago, so I ran nucmer and got the SNPs output using show-snps. This output turned out to be troublesome because it's not a VCF file. I was able to convert the SNPs using a script I found here.

My questions:

  1. The mummer tools have been around for quite a while -- would you recommend something else, or are they still current?
  2. I heard bwa-mem can also now align whole microbial genomes -- anyone have any experience with this?

Thanks for any advice!

ADD COMMENTlink written 3.2 years ago by Lina F190
1

Indeed, MUMmer has been around for a while, but in addition to being a good tool from the start, it has been updated constantly, and MUMmer 4 is on the works.

Although bwa mem can align long(ish) sequences, there is a cap at about 10Mb, and I think query and subject need to be pretty similar, otherwise performance degrades. Here is a (somewhat old, so may be outdated) blog post from BWA author. minimap2 is probably a better option.

By the way, as said on the first blog post I linked, LAST is good for very big sequences, and it is really fast.

ADD REPLYlink written 2.5 years ago by h.mon31k
1
gravatar for genomax
3.2 years ago by
genomax91k
United States
genomax91k wrote:

Mauve is the first choice for this type of a thing. LASTZ also if you want to do stricter alignments.

ADD COMMENTlink written 3.2 years ago by genomax91k

Great, thanks for the suggestion, I will take a look!

ADD REPLYlink written 3.2 years ago by Lina F190
1

I would use MUMmer over Mauve..

ADD REPLYlink written 3.2 years ago by 5heikki9.0k
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