data-schema.md

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