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本数据集为针对所有潜在病毒序列完成屏蔽处理的小鼠基因组（GRCm38）版本。如需获取人类参考基因组的病毒屏蔽数据库，请参阅《Virus+ Masked Human Genome》。以下为生成该额外病毒序列屏蔽参考数据库所用的命令：<strong>1) 下载所有RefSeq及邻接核苷酸记录：</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) 使用bbtools工具套件中的shred.sh程序切割下载的病毒基因组：</strong> shred.sh in=refseq_virus_reformated.fasta out=virus_shred.fasta.gz length=85 minlength=75 overlap=30 <strong>3) 使用bbtools工具套件中的bbmap.sh程序，将切割后的病毒序列比对至GRCm38小鼠基因组：</strong> bbmap.sh ref=GRCm38.fa.gz in=virus_shred.fasta.gz outm=map_mouse_all_viruses.sam minid=0.90 <strong>4) 使用bbtools工具套件中的bbmask.sh程序，从GRCm38基因组中屏蔽已比对上的病毒序列区域：</strong> bbmask.sh in=GRCm38.fa.gz out=GRCm38_virus_masked.fasta.gz sam=map_mouse_all_viruses.sam <strong>5) 使用seqkit工具移除所有N碱基以进一步压缩文件体积：</strong><br> seqkit -is replace -p "n" -r "" GRCm38_virus_masked.fasta.gz &gt; mouse_virus_masked.fasta_Ns_removed.gz <strong>附加参考文献：</strong> bbtools seqkit NCBI Virus Genome RefSeq