Re-calling the same event model -- improvements over 10 months

[ymc]

Thanks for your reply. The third graph doesn't seem to be an obvious improvement over the second one. It seems to me it just substituted one type of error with another type.

[gringer]

I used a custom R script for generating the graph, which works on a pairwise alignment of two sequences. The reference sequence appears at the 0 line in the graph (the top letters), and any substitutions appears underneath that, colour-coded depending on the three different types of substitutions (purine/pyrimidine, methyl/keto, strong/weak). Insertions appear as chartreuse wedges above the reference sequence, and deletions are steel blue triangles that exclude reference sequences.

I've attached the script I used to create an earlier graph with the same appearance (Image 5 in that script).

Flow cell and sequencing kits are obviously the same for all sequences, and were current on 2014-Oct-03: R7.3 flow cell, and I think SQK-MAP003.

I'm not sure about Metrichor, it was just whatever was current at the time. According to the Fast5 files, the first sequence was chimaera v1.2.2, the middle sequence was chimaera v1.6.3, and the third sequence was chimaera v1.14.4 with dragonet v1.14.2.

[ymc]

How do I make sense of this graph? What software was used to generate it?

What are the versions of Flowcell, SQK-MAP, Metrichor for each of them?

[gringer]

People seem to be interested in the error rate of the MinION. I'd like to put this image up to demonstrate one of the reasons why error rate is a fickle beast to calculate:



This is exactly the same event signal model (combination of current and dwell time inside the pore) recalled at three separate times over the past year. I've selected a small region covering a homopolymer sequence to make the mapping changes more impressive and easier to see. The reference sequence is shown in the middle (at the 0 line), with changes shown above and below the sequence.