Differences between cgmlst-dists and (commercial) Ridom SeqSphere distance matrix #17
Description
Dear all,
I've ran a sample of Illumina data on (the commercial suite) Ridom SeqSphere which does automatic fastq filtering, assembly (skesa in this case) and cgMLST analysis (scheme for Klebsiella pneumoniae).
I downloaded the same cgmlst scheme off of cgmlst.org (which is curated by Ridom) and ran the ChewBBACA analysis, and used cgmlst-dists to obtain the distance matrix. I get slighly different results, even though I input the same fasta files.
The only option I could identify in Ridom is using pairwise ignore missing values. I was wondering what is the default behavior of cgmlst-dists and if there are any options to obtain more similar results to Ridom or how to critically read the differences, as these point to differing results and impact reproducibility of results.
Thank you very much!
Alex