Virus+ Sequence Masked Mouse Reference Genome (GRCm38)

A version of the mouse genome (GRCm38) masked for all possible viral sequences.

See Virus+ Masked Human Genome for a masked human reference database.

The following commands were used to generate the additional virus sequence masked reference database:

1) Download all RefSeq and Neighbor nucleotide records:

https://www.ncbi.nlm.nih.gov/nuccore/?term=Viruses[Organism]%20NOT%20cellular%20organisms[ORGN]%20NOT%20wgs[PROP]%20NOT%20gbdiv%20syn[prop]%20AND%20(srcdb_refseq[PROP]%20OR%20nuccore%20genome%20samespecies[Filter])

2) Shred the downloaded viral genomes using shred.sh from the bbtools package

shred.sh in=refseq_virus_reformated.fasta out=virus_shred.fasta.gz length=85 minlength=75 overlap=30

3) Map shredded virus sequence to the GRCm38 genome using bbmap.sh from the bbtools package

bbmap.sh ref=GRCm38.fa.gz in=virus_shred.fasta.gz outm=map_mouse_all_viruses.sam minid=0.90

4) Mask virus sequenced mapped regions from the GRCm38 genome using bbmask.sh from the bbtools package

bbmask.sh in=GRCm38.fa.gz out=GRCm38_virus_masked.fasta.gz sam=map_mouse_all_viruses.sam

5) Remove all N's to further reduce file size using seqkit
seqkit -is replace -p "n" -r "" GRCm38_virus_masked.fasta.gz  > mouse_virus_masked.fasta_Ns_removed.gz

Additional References:

1. bbtools
2. seqkit
3. NCBI Virus Genome RefSeq