Where can I find NGS data to test alignment and SNP detection tool

Question

[somon_955]

Hi, I want to do carry out SNP detection on genomic data which has to be aligned with an in-house tool. I have to check how this tool performs with respect to other alignment tools, and whether it improves snp detection.

Any ideas wherefrom to download the genomic data (fastq), which I can then align and check for SNPs? Is it possible to find NGS data used in publications, so that I can compare if there is any difference in the detection SNPs with our tools vs existing tools?

I am new to genomics - any suggestion will be helpful.

Thanks.

[Benn]

Did you check the 1000 genomes already? They have a lot of data available on their ftp.

[WouterDeCoster]

Damn, by looking for the links you beat me by a few minutes ;-)

[Benn]

Haha, I didn't know we were in competition ;P

Answer 1

[WouterDeCoster]

Data is available from many 1000 genome samples, including "famous" samples such as the Yoruba trio (na19240 etc). Data can be accessed http://www.internationalgenome.org/data, for example http://www.internationalgenome.org/data-portal/sample/NA19240

Answer 2

[Zaag]

You can download a dataset and upload your results to compare them with other pipelines. I believe this is not real sequencing data, but a reference that's cut up to get 'reads' of a certain length.

http://www.bioplanet.com/gcat

And the Genome in a bottle consortium has all kinds of 'golden standard' datasets you can use (actual sequencing data):

https://www.nist.gov/news-events/news/2016/09/nist-releases-new-family-standardized-genomes

Answer 3

[chen]

best place to find real data: NCBI SRA https://www.ncbi.nlm.nih.gov/sra/

[WouterDeCoster]

The biggest problem with "real data" is that there is no "truth set": variants which you can be sure of. The data from the genome in a bottle consortium is a set of golden standards data with extensive validation and confirmation using different technologies.