Reference-Guided Assembly Scaffolding With RaGOO

Posted on Thu 31 January 2019 in genomics • Tagged with genome assembly, genomics, plantsLeave a comment

Nowadays, assembling large eukaryotic genomes is more accessible than ever. This is in large part due to the fact that Oxford Nanopore Technologies (ONT) has made tremendous strides towards improving the throughput of their sequencers.

For example, Michael et al. recently described the ability to obtain highly-contiguous Arabidopsis thaliana assemblies from a single MinION flow-cell. It's also becoming clear that the PromethION is reaching insanely high levels of throughput, producing Terabases of data in just days.

Continue reading

Sugarcane Genomics Review

Posted on Mon 29 January 2018 in genomics • Tagged with plants, genomicsLeave a comment

I have recently started working on a sugarcane genome assembly project, so I figured I would share some interesting points from my literature review. Sugarcane is obviously a very economically important crop, having applications in both food and energy production. Despite this economic importance, genomic resources are lacking for sugarcane due to the complexity of the genomes of modern cultivars. Let's look into the specifics of why that is.

Continue reading