Ion Torrent sample data

Question

[Milan Domazet]

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!

Answer 1

[Keith Callenberg]

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.

[Milan Domazet]

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

Answer 2

[matted]

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.