A (growing) collection of information contributed by Genomics Aotearoa members.

See the Troubleshooting Guide for handy tips, tricks and tutotials. Our Scripting and Programming Tips page has useful information to help with scripting and coding.

ESR has been performing benchmarking experiments with GPU base calling of Oxford Nanopore data. The below documentation outlines the current results.

GPU basecalling benchmarks

Dr Miles Benton
ESR (Institute of Environmental Science NZ)
14/05/2019

Dr Ann McCartney, a Genomics Aotearoa funded researcher at Manaaki Whenua Landcare Research, has contributed some information based on her experiences on working with Oxford Nanopore sequencing data:

Re-base-calling my Oxford Nanopore data?

Dr Ann McCartney
Manaaki Whenua / Landcare Research
26/09/2019

Some musings as I go through a number of different clustering algorithms in the python sklearn library.

Bin cluster refinement

Dr David Waite
University of Auckland
22/11/2019

A growing collection of notes and benchmarking nanopore basecalling on the Jetson Xavier.

Xavier basecalling benchmarks

Dr Miles Benton
ESR (Institute of Environmental Science NZ)
16/01/2020

A test run of different combinations of assemblers, read mapping, and binning tools for determining the best recovery of MAGs from estuarine sediment metagenomes.

Metagenomic assembly and binning with ONT

Dr David Waite
University of Auckland
12/02/2020