SPADA Meeting Book

as Primer-BLAST or ThermoBLAST using a combined database of full-length and partial 307 genomes. In instances where there is an abundance of sequencing for a particular gene (e.g., 16S 308 ribosomal RNA, a particular conserved virulence factor, or a toxin gene) from an organism, it is 309 important to include in the inclusivity database only sequences (complete or partial) that contain 310 that gene of interest. 311 The trend in next generation sequencing is toward production of a large number of draft 312 microbial genomes with multiple contigs due to the low cost of generating short read sequences. 313 Although, complete finished genomes can be generated by adding long read sequences obtained 314 from platforms such as PacBio or Oxford Nanopore with nominal additional cost, the general 315 trend appears to be a decline over time in the number of complete finished genomes compared to 316 draft genomes (Figure 6). At the same time, perhaps, with smaller genomes (e.g., viruses) there 317 may be an increase in full length genomes over time. Along with the expected exponential 318 increase in the size of databases will be a growing demand on the computational resources to 319 handle such larger databases. 320

Commented [SS1]: Can we substantiate this?

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