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Viral sequences
Keiran Raine edited this page Apr 18, 2016
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4 revisions
The viral sequence reference should be downloaded from NCBI and decompressed:
curl -sSL ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz \
| gunzip -c > viral.genomic.fa
curl -sSL ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.2.1.genomic.fna.gz \
| gunzip -c >> viral.genomic.fa
Then convert to 2bit fasta files, see Microbial Sequences for binary:
./faToTwoBit -noMask viral.genomic.fa 2bit/viral.genomic.merged.fa.2bit