Pipelines to do MinION sequencing of Zika virus

Sample metadata

Sample metadata for the Zika pipeline arrives in the samples/ directory. This should be mounted to samples/ in the Docker container.

  • samples/
    • samples.tsv - line list of sample metadata
    • runs.tsv - line list of run metadata

samples.tsv

Must be tsv formatted. Keyed off of column headers rather than column order. sample_id is keyed to accession in fauna because these lack Genbank accessions.

sample_idstraincollection_datecountrydivisionlocation
VI1USVI/1/20162016-09-28usvisaint_croixsaint_croix

runs.tsv

Must be tsv formatted. Keyed off of column headers rather than column order.

run_namebarcode_idsample_idprimer_scheme
usvi-library1-2016-12-10NB01VI1v2_500.amplicons.ver2