ZIKA Pipeline Notes

Setup

Make sure environment variables for connecting to fauna are set.

Upload via ViPR and update citations

ViPR sequences

Download sequences
- Select year >= 2013 and genome length >= 5000
- Download as Genome Fasta
- Set Custom Format Fields to 0: GenBank Accession, 1: Strain Name, 2: Segment, 3: Date, 4: Host, 5: Country, 6: Subtype, 7: Virus Species
- May also use the ViPR API

  curl "https://www.viprbrc.org/brc/api/sequence?datatype=genome&family=flavi&species=Zika%20virus&fromyear=2013&minlength=5000&metadata=genbank,strainname,segment,date,host,country,genotype,species&output=fasta" |\
  tr '-' '_' |\
  tr ' ' '_' |\
  sed 's:N/A:NA:g' >\
  GenomicFastaResults.fasta

The search-and-replace commands (tr, sed) are necessary because the API downloads fasta headers similar to:

but need to match the GUI downloaded headers similar to:

Move downloaded sequences to fauna/data
Extract GenomicFastaResults.tar.gz and rename the extracted file to GenomicFastaResults.fasta
Upload to vdb database
- python3 vdb/zika_upload.py -db vdb -v zika --source genbank --locus genome --fname GenomicFastaResults.fasta

Update

Update citation fields
- python3 vdb/zika_update.py -db vdb -v zika --update_citations
- updates authors, title, url, journal and puburl fields from genbank files
- If you get ERROR: Couldn't connect with entrez, please run again just run command again

Download from Fauna, parse, compress and push to S3

Download from Fauna

python3 vdb/download.py \
  --database vdb \
  --virus zika \
  --fasta_fields strain virus accession collection_date region country division location source locus authors url title journal puburl \
  --resolve_method choose_genbank \
  --fstem zika

This results in the file data/zika.fasta with FASTA header ordered as above.

Parse

augur parse \
  --sequences data/zika.fasta \
  --output-sequences data/sequences.fasta \
  --output-metadata data/metadata.tsv \
  --fields strain virus accession date region country division city db segment authors url title journal paper_url \
  --prettify-fields region country division city

This results in the files data/sequences.fasta and data/metadata.tsv.

Compress

zstd -T0 data/sequences.fasta
zstd -T0 data/metadata.tsv

This results in the files data/sequences.fasta.zst and data/metadata.tsv.zst.

Push to S3

nextstrain remote upload s3://nextstrain-data/files/zika/ data/sequences.fasta.zst data/metadata.tsv.zst

This pushes files to S3 to be made available at https://data.nextstrain.org/files/zika/sequences.fasta.zst and https://data.nextstrain.org/files/zika/metadata.tsv.zst.

Run zika workflow

See instructions at https://github.com/nextstrain/zika.