deGRIT: a program to polish genome assemblies using transcriptome data

The program described herein is available from https://github.com/zkstewart/deGRIT. Background to the development of deGRIT PacBio-based genomes have huge advantages over Illumina-based assemblies. The long PacBio (or Oxford Nanopore) reads result in significantly more contiguous assemblies, meaning better N50 scores and, hopefully, better representation of genes in your assembly. The error-prone nature of these long reads … Continue reading deGRIT: a program to polish genome assemblies using transcriptome data

Polishing PacBio assemblies with Arrow and Pilon

My current project involves the assembly of sea anemone genomes from PacBio long reads. From the start to where I am now, I've encountered a lot of bugs, errors, and other things I've had to spend minutes to days trying to resolve. Polishing assemblies is one of those things which took a few days all … Continue reading Polishing PacBio assemblies with Arrow and Pilon

Running fastStructure and associated difficulties

Recently, I have been providing a bit of bioinformatic assistance to another researcher at QUT. As part of this, I have had to learn how to format data inputs, among other things, to get fastStructure to work. fastStructure is a program used for population genetics analysis (a fair bit outside of what I am currently … Continue reading Running fastStructure and associated difficulties