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data-schema.md

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Raw

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.

sample_id strain collection_date country division location
ZBRD116 ZBRD116 2015-08-28 brazil alagoas arapiraca
ZBRC301 ZBRC301 2015-05-13 brazil pernambuco paulista

runs.tsv

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

run_name barcode_id sample_id primer_scheme
library1 NB01 ZBRD116 v2_500.amplicons.ver2