AVIAN_FLU.md

Avian flu pipeline notes

VDB

Upload documents to VDB

Upload from GISAID

1. Download sequences and meta information from GISAID

• In EPIFLU, select for H9N2, H7N9, or H5 sequences, select HA as required segment, select Submission Date >= last upload date to vdb
• Download at most 5000 isolates at a time, may have to split downloads by submission date
• Download Isolates as XLS with YYYY-MM-DD date format
• Download Isolates as "Sequences (DNA) as FASTA"
  • Select all DNA, except HE and PE
  • Fasta Header as 0: DNA Accession no., 1: Isolate name, 2: Isolate ID, 3: Segment, 4: Passage details/history, 5: Submitting lab
  • DNA Accession no. | Isolate name | Isolate ID | Segment | Passage details/history | DNA INSDC

2. Move files to fauna/data as gisaid_epiflu.xls and gisaid_epiflu.fasta.
3. Upload to vdb database

• python3 vdb/avian_flu_upload.py -db vdb -v avian_flu --data_source gisaid --source gisaid --fname gisaid_epiflu
• Recommend running with --preview to confirm strain names and locations are correctly parsed before uploading
  • Can add to geo_synonyms file and flu_fix_location_label file to fix some of the formatting.

Upload from IRD

1. Download sequences from IRD

• Search for Sequences and strains
• Select Data Type as Strain
• Enter either "H5N1" or "H7N9" under Subtype
• Click Search
• Click download all ...
• Download "Segment FASTA" as GenomicFastaResults.fasta. Select "Custom format", select all and add.

2. Move file to fauna/data as GenomicFastaResults.fasta.
3. Upload to vdb database

• python3 vdb/avian_flu_upload.py -db vdb -v avian_flu --data_source ird --source ird --fname GenomicFastaResults.fasta
• Recommend running with --preview to confirm strain names and locations are correctly parsed before uploading
  • Can add to geo_synonyms file and flu_fix_location_label file to fix some of the formatting.

Download documents from VDB

python3 vdb/avian_flu_download.py -db vdb -v avian_flu --select locus:HA subtype:h7n9 --fstem h7n9_ha