Anyone here uses MUMmerGPU?

[brianlamx]

Hi I have problem building suffix trees using MUMmerGPU with human chromosomes. I tried with chr1 and chr22 but no luck so far. When I tried with an artificial sequence it works. Is it that the Ns are stopping it from working properly?

TA

B

[Torst]

Hi I have problem building suffix trees using MUMmerGPU with human chromosomes. I tried with chr1 and chr22 but no luck so far.

Does it work with regular MUMmer?

Will MUMmerGPU really offer much improvement in speed?

[spenthil]

http://www.biomedcentral.com/1471-2105/8/474/figure/F6

(from: http://www.biomedcentral.com/1471-2105/8/474)

[Melissa]

Hi I have problem building suffix trees using MUMmerGPU with human chromosomes. I tried with chr1 and chr22 but no luck so far. When I tried with an artificial sequence it works. Is it that the Ns are stopping it from working properly?

TA

B

The Ns won't affect. Just wanna check with you that you're using only one sequence to construct the suffix tree. I think MummerGPU don't support multiple sequences as reference.

[Torst]

http://www.biomedcentral.com/1471-2105/8/474/figure/F6

Are you mapping READS to the human genome, or comparing contigs?

If using reads, there are much better tools like BWA etc that will give 1000x speedups compared to Mummer. If mapping large sequences, the GPUMummer gives no speedup compared to Mummer (see the graph).

Don't put yourself through pain unless you are forced to!