Nanopore

PromethION human genome NA19240

TLDR: we sequenced a human genome, NA19240, to 80x coverage using the Oxford Nanopore PromethION. The data is freely available on ENA.


We have been sequencing on Oxford Nanopore PromethION since February. Our main interest is in structural variation in the context of neurodegenerative diseases such as Alzheimer Disease and Frontotemporal Dementia, but for benchmarking and tool development we have sequenced the Yoruba reference genome NA19240 to 80x coverage (258Gigabases) using 5 flowcells, a Yoruban individual part of the HapMap and 1000 genomes project and well documented (Steinberg et al 2016Chaisson et al 2017, and many more).

The ENA project ID is PRJEB26791, the most recent basecalls (guppy 1.4.0) can be found here. We have also generated two runs on MinION for comparison, which are also available.

Summary

Run DNA shearing BluePippin size selection Library prep kit Yield [Gbase] ENA accession
P1 unsheared >10kb LSK109 59 ERR2631600
P2 MegaRuptor 20kb >8kb LSK109 69 ERR2631601
P3 unsheared >10kb LSK109 29 ERR2631602
P4 unsheared >10kb LSK108 29 ERR2631603
P5 MegaRuptor 20kb >6kb LSK109 72 ERR2631604
M1 unsheared >10kb LSK109 4.8 ERR2683660
M2 unsheared >10kb LSK109 7.9 ERR2683661

Plots

The plots below were generated using NanoComp and NanoPlot.

NanoComp_total_throughput

NanoComp_log_length\

TimeQualityViolinPlot

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s