Question: Ion Torrent sample data
1
gravatar for Milan Domazet
4.1 years ago by
Milan Domazet10 wrote:

Hello everyone,

I am making a Ion Torrent pipeline by using tools from latest torrent suite. I am having hard time finding any sample data (with reference it was aligned against) using which I can do the tests (mapping, indexing and variant calling).

Are you familiar with any FTPs or something similar where I could find these?

Cheers!

ion sample tool alignment torrent • 2.3k views
ADD COMMENTlink modified 4.1 years ago by Keith Callenberg900 • written 4.1 years ago by Milan Domazet10
4
gravatar for Keith Callenberg
4.1 years ago by
Pittsburgh, PA
Keith Callenberg900 wrote:

There are two data sets from the NIST Genome in a Bottle project that would be good tests for Ion Torrent pipelines:

Ashkenazi trio:
ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/AshkenazimTrio/
There is an ion_exome directory inside each of the trio members directories with Ion Torrent data.

NA12878 cell line:
ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/ion_exome/

These are particularly nice because there is plenty of reference material on these samples so that you can validate your results.

ADD COMMENTlink written 4.1 years ago by Keith Callenberg900

Thanks a lot! Second link did the trick. :)

ADD REPLYlink written 4.1 years ago by Milan Domazet10
2
gravatar for matted
4.1 years ago by
matted7.2k
Boston, United States
matted7.2k wrote:

This may not get you everything that you want, but it could be a start.

DNAnexus has an SRA search engine (sra.dnanexus.com) where you can filter by instrument type.  Using it, I see 683 studies from Ion PGM or Proton machines, 29 of which are human samples.  Going through some of these may lead you to good benchmark datasets.

 

ADD COMMENTlink written 4.1 years ago by matted7.2k
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