VirusDiscoveryProject

Software, architecture, and data index design for the 2018/2019 Virus Discovery Project

Here we present a compromise pipeline for extracting virological information from publicly available metagenomic datasets, in order to present a usable index to the virological research community.

Look at the cool new sh*& NCBI built for us!

NCBI Blast Docker:

https://github.com/ncbi/docker/blob/blast2.8.1/blast/README.md

Theres also a nice cookbook here, with thanks to @christiam!

GS Blast dbs

BLAST Databases currently being updated to the NIH STRDES GCP bucket (gs://blast-db/)

nr, nt, etc.

Virus specific ones!

ref_viruses_rep_genomes_v5 Subset of refseq_genomes “latest_refseq[Prop] AND viruses[Organism]”

ref_viroids_rep_genomes_v5 Subset of refseq_genomes “latest_refseq[Prop] AND viroids[Organism]”

NCBI_VIV_protein_sequences_v5 nr Sergey Resenchuk supplied GI list

NCBI_VIV_nucleotide_sequences_v5 nt Sergey Resenchuk supplied GI list

CONTIGS!

XXXnumber are available from <>

Accessible using SRA toolkit