Equus caballus Project

Aim

Assess sequence polymorphism in five horse genes of interest by comparing amplicon seq data of healthy and unhealthy horses.

Genes of interest:

1. Proglucagon (GCG) gene - ENSECAG00000005660 has two gene splicing variants:

Open

1. Melanocortin 2 receptor (MC2R)

- ENSECAG00000003841 single splice variant:

Open

1. Melanocortin 4 receptor (MC4R)

- ENSECAG00000001712 has a single splice variant:

Open

1. Proopiomelanocortin (POMC)

- ENSECAG00000016388 has three splice variants:

Open

Open

1. Adiponectin (ADIPOQ)

- ENSECAG00000002962

Open

ConsGenome pipeline: Creating a conda environment

See this tutorial for additional information: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

The ConsGenome workflow requires the following tools specified in an ‘environment.yml’ file:

Creating a conda environment called ‘ConsGenome’

Activate the environment → this enables to use of the above tools. NOTE: prior to running netxflow need to activate the ConsGenome environment.

Deactivate the environment

Nextflow - ConsGenome pipeline

This is a QUT eResearch developed pipeline for 1) the de novo assembly of reference sequences (i.e., amplicon seq regions, metagenomics sequences, etc); 2) map and deduce a reference consensus genomics/transcript sequence based on HTS data collected for a given sample, and 3) identify nucleotide sequence polymorphism.

To run the pipeline prepare the following:

• index.csv - a file describing the sample ID, the path to read1 and read2 if applicable

• nextflow.config - a file to specify parameter options such as the genome/transcriptome/amplicon reference to use to map reads and predict a consensus sequence

• launch.pbs - PBS Pro script to submit the ConsGenome job to the HPC cluster

Example index.csv file:

Example nextflow.config file:

Launch.pbs script: