This repository contains the code relating to the assembly, annotation and genomic investigation into the newly sampled Hydrophis snakes H. major, H. ornatus, H. curtus (West) and H. elegans (along with already existing Hydrophis and terrestrial samples). The repository is organised into sub-directories, each of which contains the code used in the analyses, along with a summary of the overall approach.
The approximate order of the analyses are below:
- Genome assembly
- Genome annotation
- Phylogenetics
- Genome synteny
- Ortholog detection
- Ortholog annotation
- Selection testing
- GO over-representation
Additional directories include the following;
The data directory contains data that are not specific to any one analysis,
while the figure and tables directories contain the figures and tables that
are found in the manuscript.
A few of the analyses listed above make use of custom Nextflow workflows that can be found here. Specific details about the Nextflow workflows can be found at the wiki page. Some custom tools are also used for processing some output data which can be found here:
I've tried to be as detailed as possible, however this is a large project and it's difficult to include everything. Many auxilliary files from analyses are included in this directory, however some files are too large and could not be uploaded. Additionally, some scripts have been edited down to include their main function calls rather than include additional information that is not relevant.
Ludington, A.J., Hammond, J.M., Breen, J. et al. New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21, 284 (2023). https://doi.org/10.1186/s12915-023-01772-2
Please cite the paper if you find any of the code/work helpful.