Collate samplesheets

[mbhall88]

For the main assessment we will need a collection of Illumina and Nanopore data with phenotypes.

So far, I have collated accessions for 44,880 Illumina isolates with the following phenotype information

In terms of gathering Nanopore data, a main question is whether we want to only used Nanopore data basecalled with the same version of guppy or not? This is an overarching question for the field too I guess. I am inclined to think the version doesn't matter for this kind of benchmark - provided it was basecalled with guppy. Thoughts?

One last question is whether we want to use all of the 43K Illumina isolates or just a subset based on phenotypes for certain drugs?

[mbhall88]

For Nanopore data, if I include the NY data and Peker data, we have 437 isolates with phenotype information.