Pipelines to do MinION sequencing of Zika virus

Data schema

Nanopore reads

Input data to the Zika pipeline arrives in the data/ directory. This should be mounted to data/ in the Docker container.

  • data
    • usvi-library1-2016-12-10 - library
      • raw_reads - squiggle graphs in fast5 format
      • pass - contains .fast5 files
      • basecalled_reads - basecalled with Metrichor
      • pass_demultiplex - demultiplexed basecalled reads
        • NB01 - contains .fast5 files for NB01 barcode
        • NB02 - contains .fast5 files for NB02 barcode
        • etc...
      • nonNB_demultiplexed - demultiplexed basecalled reads
        • BC01 - contains .fast5 files for BC01 barcode
        • BC02 - contains .fast5 files for BC02 barcode
        • etc...
      • fail - contains .fast5 files that weren't demultiplexed