real data for haplotype assembly problem?

[denflyson]

Dear all,

I am now working on haplotype assembly problem. I need some real data, i.e. sequence reads to test my program. Does anyone have such kind of data that can share with me? Thanks.

[flxlex]

Small genomes? Large genomes?

[denflyson]

Small genomes? Large genomes?

Both are ok. It would be better if it is on human genome.

[flxlex]

Lot's of human genome sequencing reads available, and they are all by defnition heterozygous. Check the NCBI sequence read archive, and the 1000 genomes project.

[denflyson]

Lot's of human genome sequencing reads available, and they are all by defnition heterozygous. Check the NCBI sequence read archive, and the 1000 genomes project.

Got it. Thanks.

[ymc]

You can find high coverage CEU and YRI trios here

ftp://ftp.1000genomes.ebi.ac.uk/vol1...h37_bams/data/

[denflyson]

You can find high coverage CEU and YRI trios here

ftp://ftp.1000genomes.ebi.ac.uk/vol1...h37_bams/data/

It's very helpful. Many Thanks.

[arelouse]

Dear all,

I am now working on haplotype assembly problem. I need some real data, i.e. sequence reads to test my program. Does anyone have such kind of data that can share with me? Thanks.

Hi, Denflyson, I'm also going to work on this assembly problem. But I'm new to this area and almost know nothing about its technique development and whether it's a promising approach to get haplotype using NGS data.

I have read papers about HapCut, ReFHap and HapCompass. I want to read more to understand this problem better, and then I can figure out one package and port it to a HPC platform using either multithread/MPI/CUDA stuff.

Do you have any recommendations for papers to read? Can you share some opinions about this problem? Any information will be appreciated!

Zhiqiang