A new platform called IDseq is meant to help the world's disease detectives diagnose mysterious illnesses more easily. Here's my piece on why it's important, and the likely challenges ahead.https://www.theatlantic.com/science/archive/2018/10/dashboard-disease-detectives/573034/?utm_source=twb …
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Right. The interpretation gap is huge right now.
Yup - accurate classification of reads, contaminant detection, and scoring of likely causality are by far the most critical needs - and here new tools are needed. To me IDSeq appears to be an online wrapper for preexisting tools e.g. Gsnap, rapsearch, bowtie2, etc.pic.twitter.com/JA2a9z3eUC
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Compare that overview figure to the overview of the pipeline I developed >5 years ago. Not a lot has happened since then to be honest - but of course, having a website is nice (although I think Taxonomer has that totally covered).pic.twitter.com/Py43JghElP
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Agreed that contamination quantification, spurious mappings (from eg bad db), and scoring are the hardest parts. Even with large datasets (400 px from a few hospitals, similar context and processing), we've had trouble fitting reasonable models.
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Yes, and that's before we get into all the unresolved stuff about how you effectively prepare a clinical sample for high sensitivity sequencing.
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Also the library prep and positive and negative controls need to be standardized across sites...or else disaster looms.
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