Sequencing DNA with Linux Cores and Nanopores

See the YouTube video here:

https://www.youtube.com/watch?v=CHCAb-PAqUI

Most of the files here are sequenced reads (including signal-containing FAST5 files) from sequencing runs carried out as part of preparation for my LCA 2019 talk: Sequencing DNA with Linux Cores and Nanopores.

This was a mixed yoghurt, tomato and strawberry sample. DNA was extracted using the Qiagen PowerWater kit, and concentrated using Ampure XP beads to 18ng/μl. 7.5μl of the concentrated DNA sample was then processed with the Oxford Nanopore Rapid Barcoding kit, and sequenced for 15 minutes on an Oxford Nanopore MinION.

This is a backup dataset for my demonstration at the conference, in the very likely event that sample preparation does not produce sufficient amounts of DNA on the day for a good 15-minute sequencing run. It will be updated after the conference with any additional sequencing runs that are carried out.

Preliminary FAST5 and FASTQ reads for my linux.conf.au talk are now in this repository (see archive 'LCA_2019_run.tar.gz'). Unfortunately I forgot to generate a raw file; I might see if I can do a re-run using the same sample.

The accessory Perl, R, and Python programs that I am using in my presentation can be found in my 'bioinfscripts' GitLab repository:

• https://gitlab.com/gringer/bioinfscripts

I also use LAST for sequence similarity searching during demultiplexing:

• Web interface http://lastweb.cbrc.jp
• Command line version http://last.cbrc.jp

For more details about nanopore sequencing, see Oxford Nanopore's website, and my nanopore notes:

• https://gringer.gitlab.io/presentation-notes/2018/10/25/nanopore-notes/

Hand-crank centrifuge model:

• https://www.thingiverse.com/thing:1807878

Read demultiplexing protocol:

• https://dx.doi.org/10.17504/protocols.io.xj3fkqn

If you're interested in purchasing the "genes in a T-shirt" that I wore during my talk, here's the Zazzle link to my virtual shop:

https://www.zazzle.co.nz/gringene