CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Saymon Akther; Edgaras Bezrucenkovas; Brian Sulkow; Christopher Panlasigui; Li Li; Weigang Qiu; Lia Di

For the Covid-19 genome browser, we download genomic sequences and associated 85 metadata of SARS-CoV-2 isolates from GISAID (5), which are subsequently parsed with a PY-86 THON script ("parse-metadata.ipynb"; all scripts available in GitHub repository http://cov.ge-87 nometracker.org). We use a custom BASH script ("align-genome.sh") to align each genome to 88 an NCBI reference genome (isolate Wuhan-Hu-1, GenBank accession NC_045512) with Nu- The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.10.036343 doi: bioRxiv preprint script ("impute-hap.pl") is used to trim SNP sites at genome ends where missing bases are com-94 mon, discard haplotypes with more than 10% missing bases, (optionally) impute missing bases 95 of a haplotype with homologous bases from a closest haplotype (19), and identify unique haplo-96 types using the BioPerl package Bio::SimpleAlign (20). To root the haplotype network, we in-97 clude the genome of a closely related bat isolate (RaTG13, GenBank accession MN996532) (1) 98 as the outgroup (using however only nucleotides at the SNP sites present among human iso-99 lates). 100