Cortex for Oxford Nanopore data

[niru.ch...@claritasgenomics.com]

We are planning to try cortex on Oxford Nanopore data. Has anyone tried this before?

[Zamin Iqbal]

I've not tried very hard. In short kmer-based genotyping does work (see Mykrobe.com and nature.com/ncomms/2015/151221/ncomms10063/full/ncomms10063.html) but Cortex variant discovery is not likely to work well because I don't think the graph cleaning will work very well. I've only done limited analysis of this. If you put the reads through Gene Myers' scrubber thing and removed chunks of reads that are clearly bad, then you might get good results ...

regards

Zam

PS Sorry for slow response.