Hi everyone,
I'm reaching out for some clarity on the ConClave scoring method as described in Philip Clausen's work (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6). While I understand the general idea that ConClave scoring involves initially accepting all best-matching templates for all best-matching query sequences and then summing the alignment scores for each template candidate, I'm stuck on a specific detail.
In particular, Step 4 in Figure 1 of the paper outlines the ConClave scoring process starting with a query alignment that produces an "Aln score" of 95, which is then aligned with multiple templates (e.g., 1, 2, 6, and 70). The ConClave score for each template is then calculated, such as 1402 for template 1 and 989 for template 2. I understand that 1402 is the sum of the alignment scores, but I'm confused about how the "Aln score" of 95 relates to the ConClave score of 1402. Could someone explain the exact nature of the "Aln score"?
Lastly, according to the paper, KMA uses data from 2012, which is before nanopore sequencing was around, and was initially designed for short-read sequencing. We use a nanopore device in our lab. Does anyone have experience or insights on whether KMA can be successfully used with nanopore reads?
Thanks in advance for your help!
