Evaluating an Upper Respiratory Disease Panel on the Portable MinION Sequencer

Wanda J. Lyon; Zachary K. Smith; Brian Grier; James Baldwin; Clarise R. Starr

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/436600 doi: bioRxiv preprint database of viral and bacterial genomes [27, 40] . All genomes, viral and bacterial were downloaded from NCBI Ref Seq (May, 2015) and were used to build the Kraken database (version 0.10.4) with k=31. Bracken was used for reassign alignments to the species level and visualization was accomplished with Krona [31] using the highest of number of hits (lowest evalue) or Metrichor's WIMP. Viral and bacterial databases were obtained from NCBI viral genomes resource [2] . Read percentage identity is defined as 100 * matches/ (matches + deletions + insertions + mismatches). Fraction of reads aligned are defined as (alignment length + insertions -deletions)/ (alignment length + unaligned length -deletions + insertions) [21] . was used verify the Metrichor WIMP identification. All of the organisms listed above were successfully sequenced on the MinION and identified correctly using the WIMP application, uses a databank of reference sequences for viruses, bacteria, and fungi. Figure 1 shows an a representative example of the data analysis for an influenza A H1N1 isolate listed in Table 1 . All viruses and bacteria listed in Tables 2 and 3 were correctly identified using WIMP. In addition, BWA and SAM Tools was used to verify that the alignment for each of the isolates listed in Tables 2.