EBOLA Pipeline Notes

Upload documents to VDB

1. Download Ebola sequence data from https://github.com/ebov/space-time/tree/master/Data
2. Move Makona_1610_genomes_genomes.fasta sequences to fauna/data
3. Replace SLE with sierra_leone, LBR with liberia and GIN with guinea
4. Replace sierra_leone\|\? with sierra_leone|sierra_leone, liberia\|\? with liberia|liberia and guinea\|\? with guinea|guinea
5. Replace sierra_leone\|\| with sierra_leone|sierra_leone|, liberia\|\| with liberia|liberia| and guinea\|\| with guinea|guinea|
6. Upload to vdb database
   • python vdb/ebola_upload.py -db vdb -v ebola --source genbank --locus genome --fname Makona_1610_genomes_genbank.fasta
7. Hand edit author and url info into other 153 genomes
8. Upload to vdb database
   • python vdb/ebola_upload.py -db vdb -v ebola --source genbank --locus genome --fname Makona_1610_genomes_quick.fasta --authors "Quick et al" --url https://github.com/nickloman/ebov/

Update

1. Update citation fields
   • python vdb/ebola_update.py -db vdb -v ebola --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 documents from VDB

• python vdb/ebola_download.py -db vdb -v ebola --fstem ebola --resolve_method choose_genbank