4 ms·

The hardest part of genomics for me has honestly been figuring out which open source poorly maintained tool I should use for a particular problem. and which opt

The hardest part of genomics for me has honestly been figuring out which open source poorly maintained tool I should use for a particular problem. and which options should be run and how the data need to be preprocessed before hand. I mean has anyone ever actually read the documentation of the GATK? It is famously dreadful. And that's professionally maintained. Honestly a nice addition here would be a "so you want to" with snippets of raw FASTQ or VCF data and working code for various operations, maybe with an accompanying Docker container.

xyhopguy 7y ago
have you ever looked at the test suites for Picard? All regression tests and the library is OO hell lols I was taught a decade ago that rolling your own in genomics isn't as bad of a decision as it seems.
- searine 7y ago
  >I was taught a decade ago that rolling your own in genomics isn't as bad of a decision as it seems. Famous last words.
- Ultimatt 7y ago
  This is sadly very true, especially if you have any real software training.
dekhn 7y ago
I feel like ADAM (https://github.com/bigdatagenomics/adam https://github.com/bigdatagenomics/adam) is a huge step in the right direction. You convert from standard genomics format to Parquet and then work with the resulting data in spark with genomics-specific libraries. My experience has been translating domain data into spark has a 100X improvement in data analysis.
anderspitman 7y ago
TRUWL had a poster at the Biology of Genomes conference last week. Sounds like they're working on this problem. I hope they succeed, because it really needs to be solved. [0] https://truwl.com/ https://truwl.com/
attractivechaos 7y ago
> I mean has anyone ever actually read the documentation of the GATK? It is famously dreadful. Reference for "famously"?