Question: Speeding up NUCmer for de novo contig to reference alignment
1
gravatar for lkw222
3.3 years ago by
lkw22230
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 • 1.5k views
ADD COMMENTlink modified 3.3 years ago by ALchEmiXt1.9k • written 3.3 years ago by lkw22230
1
gravatar for sst
3.3 years ago by
sst20
United Kingdom
sst20 wrote:

Never tried it, but http://bioinformatics.oxfordjournals.org/content/31/4/509.long claims to be an efficient drop-in replacement for MUMmer.

ADD COMMENTlink modified 3.3 years ago • written 3.3 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 2.0 years ago by cmdcolin1.2k
0
gravatar for ALchEmiXt
3.3 years ago by
ALchEmiXt1.9k
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 3.3 years ago • written 3.3 years ago by ALchEmiXt1.9k
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