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: <strong>1) Download all RefSeq and Neighbor nucleotide records:</strong> 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]) <strong>2) Shred the downloaded viral genomes using shred.sh from the bbtools package</strong> shred.sh in=refseq_virus_reformated.fasta out=virus_shred.fasta.gz length=85 minlength=75 overlap=30 <strong>3) Map shredded virus sequence to the GRCm38</strong><strong> genome using bbmap.sh from the bbtools package</strong> bbmap.sh ref=GRCm38.fa.gz in=virus_shred.fasta.gz outm=map_mouse_all_viruses.sam minid=0.90 <strong>4) Mask virus sequenced mapped regions from the GRCm38 genome using bbmask.sh from the bbtools package</strong> bbmask.sh in=GRCm38.fa.gz out=GRCm38_virus_masked.fasta.gz sam=map_mouse_all_viruses.sam <strong>5) Remove all N's to further reduce file size using seqkit</strong><br> seqkit -is replace -p "n" -r "" GRCm38_virus_masked.fasta.gz &gt; mouse_virus_masked.fasta_Ns_removed.gz <strong>Additional References:</strong> bbtools seqkit NCBI Virus Genome RefSeq