Class overview

In this part of the workshop, we will focus on certain aspects of comparative genomics. Specifically, our attention will be directed towards whole genome alignment (WGA) as a tool for investigating the changes occurring in different regions of the genome that are of interest to us. Additionally, we will explore the identification of potential regulatory elements in intergenic regions. All of this will be done in the context of the radiation of the neotropical Heliconius butterflies.

Cicconardi F, Milanetti E, Pinheiro de Castro ÉC, Mazo-Vargas A, Van Belleghem SM, Ruggieri AA, Rastas P, Hanly J, Evans E, Jiggins CD, McMillan OW, Papa R, di Marino D, Martin A, Montgomery SH (2022). “Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies”. BioRxiv

Dependencies

Below is a breakdown of the required dependencies.

- Kent toolkit. All of the binaries required are available pre-compiled on the utility page. The required tools for this tutorial are wigToBigWig, gtfToGenePred, genePredToBed.

- Bedtools & Samtools

- Progressive Cactus. With it, you should also find precompiled binaries for Hal Tools.

- gffread from the Cufflink package.

- Phylogenetic Analysis with Space/Time Models (PHAST) package.

- IGV or any other genome browser of your like, to have a look at all the tracks you will generate

Make sure you put the newly created ~/bin/$MACHTYPE directory on your path.