Skip to content

data-schema.md

Latest commit

 

History

History
45 lines (33 loc) · 1.73 KB

data-schema.md

File metadata and controls

45 lines (33 loc) · 1.73 KB

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

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 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
⚡