The main focus of this repository is a "gisaid_script" to aid submission of SARS-CoV-2 genome sequences prepared by the WA DOH PHL to the GISAID sequence repository, for use in public health surveillance work during the COVID-19 pandemic.
The script requires a single positional arg as input: the GISAID username of the person submitting the sequences. In addition, it requires two input files to function:
- A TSV/Excel dump of the latest sample inputs from the DOH "Dashboard" tracking sample statuses
- This file is needed primarily for the updated virus name field to identify the samples once published, but also for metadata required by GISAID
- A TSV/Excel table of results from the Terra bioinformatics platform
- This table contains relevant QC metrics for assessing the suitability of genome publication, as well as links to the genome sequences within a Google Cloud Storage container
The absolute paths to these files can be provided using the --terra and --dashboard flags. Alternatively, the simplest way to use it is to put both files in a common dir, as the only files containing "terra" and "dashboard" in their respective filenames, and either providing the path to this dir with --indir, or simply running the script from within that dir. More than one Terra table can be passed at a time, if desired.
The script will download all genome sequences to a new "assemblies" subdir of the current working dir. Major outputs are two files: a gisaid_metadata.csv file and an all_sequences.fa FASTA file containing the sequence data.
Also included in this repository is a second, much simpler "terra_consolidate_script", which is meant to aid combining periodically the data tables produced by Terra workflows for individual runs into a single, larger data table, to reduce clutter in the WA DOH PHL Terra workspaces.