OceanOmics – Genome assembly and marine ecology eDNA analysis
OceanOmics is a recently established program within Minderoo Foundation’s Flourishing Oceans initiative focused on the application of genomic technologies for monitoring and conservation of marine wildlife.
Area of science
Bioinformatics
Systems used
Nimbus
Applications used
blast, R, fastqc, multiqc, singularity, slurm, miniconda, mamba, python
Partner Institution: The Minnderoo Foundation|
Project Code: A000612
The Challenge
Identifying marine vertebrates based on environmental DNA in seawater samples, the challenge is to build reproducible bioinformatics pipelines to analyse such data.
The Solution
The development of an automated pipeline for pre-processing, filtering and taxonomic annotation of samples.
The Outcome
By accessing Pawsey’s Nimbus platform, I ambe able to test and establish bioinformatics pipelines and workflows to advance marine biodiversity analyses using different sequencing protocols. The work involves the application of standard tools and pipelines for bioinformatics analyses (e.g. nextflow), as well as setting up containerized and reproducible workflows via singularity
