Question: Speeding up NUCmer for de novo contig to reference alignment
gravatar for lkw222
5.0 years ago by
lkw22230 wrote:

I have a de novo assembled mammalian genome (~300,000 contigs) that I want to align to a closely related existing reference genome using NUCmer from the MUMmer package. Subsequently, given the Coords output of the NUCmer alignment, I want to use something like OSLay to order and stitch together the contigs.

The problem is, NUCmer seems like it is going to take a very, very long time to run. I have split the reference genome up into single chromosomes and I am aligning all of my contigs to each chromosome (32 chromosomes, 32 jobs running at once). However, even the smallest chromosome has run over a day and is not complete. Any ideas on how to speed up the alignment?

I'm using:

nucmer --prefix bbu_vs_bt_ref_chr1 ./bt_ref_chr1.fa ./WB_2.0.fa


sequencing alignment assembly • 2.2k views
ADD COMMENTlink modified 5.0 years ago by ALchEmiXt1.9k • written 5.0 years ago by lkw22230
gravatar for sst
5.0 years ago by
United Kingdom
sst20 wrote:

Never tried it, but claims to be an efficient drop-in replacement for MUMmer.

ADD COMMENTlink modified 12 months ago by _r_am32k • written 5.0 years ago by sst20

just to improve google-ability of this page, the paper, in question here is "E-MEM: efficient computation of maximal exact matches for very large genomes "

ADD REPLYlink written 3.7 years ago by cmdcolin1.5k
gravatar for ALchEmiXt
5.0 years ago by
The Netherlands
ALchEmiXt1.9k wrote:
There is also a GPU optimized version you could try. How large is your reference and how large contigs? Monitor memory usage and increase memory... It needs to build a large suffix tree...
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by ALchEmiXt1.9k
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