There is no doubt that long read DNA sequencing is transforming genome assembly for genomes at all scales due to the ability to span repetitive elements such as the rRNA genes. For years DNA sequencing has been the choice of either low accuracy (85-95%) long reads with systematic errors (pacbio, nanopore) or high accuracy (>99.9%) […]
Author Archives: Rasmus H. Kirkegaard
AR(10)E we there yet?
Genome assembly has been a big challenge since the first methods for analysing DNA sequences saw the light of day. The challenge is primarily a result of our inability to read long fragments of DNA. With an explosion in the market for long read sequencing technologies (pacbio, nanopore, 10X, longas, etc) there is now hope […]
Why is it important to remove short molecules?
In the age of short read sequencing you could treat the cells with very harsh physical disruption as there was little chance that your DNA extraction could shear your DNA to shorter fragments than the machines could sequence. However, with the emerging long read sequencers short fragments are suddenly no fun and people have started […]
>100 Gbp on 1 flowcell outside ONT
After unboxing the Nanopore alpha-beta PromethION device some weeks ago and having our IT support/linux ninja help us integrate yet another box into the university network, we finally got around to run some PromethION sequencing again. We updated the PromethION software to Minknow 2 inserted a flowcell and it passed QC with 7000+ pores available […]
What is a good genome assembly?
With short reads you will often get fragmented but high single base accuracy assemblies and with long error prone reads you can get a single contig assembly with just a few ultra long reads but with a lot of errors due to the lower read quality. Some of these errors can be fixed by adding more coverage […]
Can you beat our Nanopore read error correction? We hope so!
Tagging of individual molecules has been used as an effective consensus error-correction strategy for Illumina data (Kivioja et al 2011, Burke et al 2016, Zhang et al 2016) and the principle is similar to the circular consensus sequencing strategy used to generate consensus reads with error rate of < 1 % on the PacBio (Travers et […]
Promethion configuration test and “reboxing”
Following our PromethION unboxing event we have finally managed to connect the machine to our University network and pass the configuration run. The configuration test demonstrates that the network can handle the data produced and transfer it fast enough to a network storage solution. Got everything up and running for @nanopore #PromethION CTC run thx to […]
Following our experiences with DNA sequencing using the MinION since 2014 as a part of the Minion (early) Access Programme (MAP), and their developers programme we applied for a spot on the PromethION Early Access Programme (PEAP) back in May 2015. The MinION was the mindblowing DNA sequencer that allows you to do long read (no […]