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A very interesting false positive variant

Today I was, just like any other day, looking at structural variants (SVs) from Oxford Nanopore PromethION data, aligned using minimap2 and called with Sniffles. I came across a 100 Mb pericentrometric inversion of chr12, called in multiple individuals and visible in the alignment in all my samples. The region is not crazily repetitive (just… Continue reading A very interesting false positive variant

Nanopore · Plotting · Python

Nanopore sequencing: percent identity over time

My NanoPlot tool includes plots showing the decline in base call quality and sequencing speed over time, see below. Sequencing speed reduction is presumably because the ATP in the fuel mix gets consumed, or pores start wearing out. However, I wondered if this lower quality near the end of the run was also reflected in… Continue reading Nanopore sequencing: percent identity over time

Nanopore · Plotting · Python

PromethION pore count and loading concentration vs yield

Highly similar to my previous post comparing read length and yield on PromethION I today checked the correlation between the pore count on the flow cell and the loading concentration with the yield. The code is highly similar and therefore not shown again. We do not see a strinking correlation between the loading molarity (in… Continue reading PromethION pore count and loading concentration vs yield

Nanopore · Plotting

PromethION sequencing in Antwerp in 2018

We started using PromethION about a year ago, but the good flow cells started arriving from February onwards. Below I have an overview of our runs so far, generated using NanoComp. I’ll blog more about these later if I have the time, but I’m finishing my PhD this month… The plots below show the yield… Continue reading PromethION sequencing in Antwerp in 2018