Haman genome alignment with short reads

[ptongyoo]

Hello, I'm a newbie for the genome sequencing research.

Does anyone have an experience in the human genome alignment with the complete genome and short reads ?

Based on my observations previously mentioned, BLAT was used for aligning the reads to the genomic region.

Can you suggest me more about the software and the computer performance to handle it?

[swbarnes2]

Do you have a 454 or a Solid, or Illumina?

I don't think that anyone uses BLAT for the short reads of Illumina or Solid. Burrows-Wheeler transforms are pretty fast algorithms, SOAP2 and Bowtie are the two most popular of those, and Bowtie seems to be edging out SOAP2. The Bowtie authors also post here sometimes, which is another plus.

Making the Burrows-Wheeler transformed genome takes a few hours, but you can download it already sorted from the Bowtie home page.

[ptongyoo]

Thanks swbarnes2, I work with the SOLEXA and SOLiD.

I have used MAQ for aligning the bacterial SOLEXA reads to the reference on 2.66 GHz, 8 GB ram before. But I not sure that my computer can handle the human genome or not.

I will look at the Bowtie and SOAP2.

[BioWizard]

Fastest Alignment

If you want to do alignment of human genome in minutes instead of hours, you can use ISAS. You will need 16GB for Illumina or 24GB for SOLiD.

What kind of computer do you have ?

[ptongyoo]

Now I use the PC which have 2.66 GHz quad core and 8 GB of RAM running on Linux ubuntu 64 bit for my work.

I think my exact question is "Is it necessary to buy a server for doing human genome alignment with the short reads ?" Cause I think the running time is not the problem for us if my computer can do the alignment but it takes whole day, it's ok.

Thanks for your helps.