Controls

Genbank

After completing the tutorial, a good next step is to run the controls build.
This build analyzes publicly available sequences in data/controls, which include recombinant (“positive”) and non-recombinant (“negative”) sequences.
Instructions for how to include the controls in your custom build are in the configuration Configuration section.

Run the workflow.
```
snakemake --profile profiles/controls
```

GISAID

For GISAID users, a comprehensive strain list is provided that includes all designated recombinants to date (XA - XBE). This dataset includes 600+ sequences, and can be used for in-depth validation and testing.
It is recommended to use the “Input for the Augur pipeline” option, to download a tar compressed archive of metadata and sequences to data/controls-gisaid/.

Prep the input metadata and sequences.

cd data/controls-gisaid
tar -xvf gisaid_auspice_input_hcov-19_*.tar
mv *sequences.fasta sequences.fasta
# Retain minimal metadata columns, to avoid non-ascii characters
 csvtk cut -t -l -f 'strain,date,country,gisaid_epi_isl,pangolin_lineage' *.metadata.tsv > metadata.tsv
cd ../..

Run the workflow.

# Option 1: Local testing
snakemake --profile profiles/controls-gisaid

# Option 2: High Performance Computing with SLURM
scripts/slurm.sh --profile profiles/controls-gisaid