Data schema

Nanopore reads

Input data to the Zika pipeline arrives in the data/ directory.

• data/
  • usvi-library1-2016-12-10/ - library
    • raw_reads/ - squiggle graphs in fast5 format; all subdirectores are written automatically by MinKNOW
      • 0/ - contains ~4000 raw .fast5 files
      • 1/ - contains ~4000 raw .fast5 files
      • etc …
    • basecalled_reads/ - basecalled with Albacore 1.0.4; all subdirectores are written automatically by Albacore
      • sequencing_summary.txt - summary of Albacore run; automatically made by Albacore
      • pipeline.log - summary of Albacore run; automatically made by Albacore
      • workspace - contains all basecalled, demultiplexed reads
        • barcode01/ - basecalled, demultiplexed reads with ONT barcode NB01
          • 0/ - contains ~4000 basecalled, demultiplexed .fast5 files
          • 1/ - contains ~4000 basecalled, demultiplexed .fast5 files
          • etc …
        • barcode02/ - basecalled, demultiplexed reads with ONT barcode NB02
          • 0/ - contains ~4000 basecalled, demultiplexed .fast5 files
          • 1/ - contains ~4000 basecalled, demultiplexed .fast5 files
          • etc …
        • …
        • barcode12/ - basecalled, demultiplexed reads with ONT barcode NB12
          • 0/ - contains ~4000 basecalled, demultiplexed .fast5 files
          • 1/ - contains ~4000 basecalled, demultiplexed .fast5 files
          • etc …
        • unclassified/ - basecalled, non-demultiplexed reads
          • 0/ - contains ~4000 basecalled, non-demultiplexed .fast5 files
          • 1/ - contains ~4000 basecalled, non-demultiplexed .fast5 files
          • etc …

Sample metadata

Sample metadata for the Zika pipeline arrives in the samples/ directory.

• 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.

runs.tsv

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