JSON output file

This page describes the contents of the gzipped JSON file log.json.gz, made when running viridian run_one_sample.

The file contains a dictionary of run details. The main entries (keys) are:

• run_summary - has high-level details on the run
• stages_completed - the progress of each main stage in the pipeline
• reads - high-level summary of read counts
• read_depth - genome coverage and read depth information
• amplicon_scheme_name - name of the identified amplicon scheme
• scheme_choice - details of the amplicon scheme scoring
• amplicons - details of the amplicon scheme that was used
• self_qc - details of read pileup information at each masked position
• sequences - consensus sequence and variations (for MSAs and tree building)

Please read on for more details about the contents of each of those entries.

run_summary

TBC

stages_completed

TBC

reads

TBC

read_depth

TBC

amplicon_scheme_name

TBC

scheme_choice

TBC

amplicons

self_qc

TBC

sequences

TBC