We receive support from the Australian Biocommons Apollo project and have used this to create genome browsers for new genomes generated by our group.

Reproducible analysis for publications

We work with large genomic, transcriptomic and proteomic data, often combining outputs from multiple analyses to generate inferences. A typical project will involve many small shell scripts, some command-line tools written in Python and lots of R code. We use github to manage this complexity, collaborate and share our work. For new projects we suggest starting with our project template.

Examples of publications with associated code repositories:

  • Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum
  • Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts.
  • Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris
  • Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae)

Nextflow pipelines

We are developing a set of pipelines in nextflow to automate core analysis tasks encountered in marine omics projects. The goal of these pipelines is to automate common processes and provide a form of working documentation representing current best-practices in the lab. Working pipelines currently include;

  • movp : Marine Omics Variant calling Pipeline. Calls SNPs and small indels from short-reads
  • moqc : Marine Omics Quality Control pipeline. Uses fastqc to report on read data quality and kraken to report on taxonomic composition (eg to detect contaminants).
  • morp : Marine Omics RNAseq Pipeline. Maps reads to a transcriptome and quantifies transcript abundance using RSEM
  • moat : Marine Omics AnnoTation pipeline. Functional annotation on a set of predicted proteins.
  • mod2s: Marine Omics DS2 Pipeline. kmer-based sample clustering

Getting setup to run these pipelines can be a little challenging. To make things easier we have produced a guide to using marine omics pipelines