Automatic Assembly For The Fungi (AAFTF) pipeline

Source:

https://github.com/stajichlab/AAFTF

Goal:

Assemble the genome of two M. alpina strains (Mortierella alpina and Mortierella sp.) sequenced at QUT.
Identify DAG (Diacyl-glycerol) and Phopholipase (PLA, PLB, PLC and/or PLD) genes

Method

De novo genome assembly of yeast genomes using the AAFTF pipeline. More information:

https://github.com/stajichlab/AAFTF

(pending) FunGAP pipeline for yeast genome annotation:

https://github.com/CompSynBioLab-KoreaUniv/FunGAP

Preliminary Results

https://wiki.qut.edu.au/display/erbts/M.+alpina+de+novo+genome+assemblies

Resources

Using conda environments:

https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

Methodology

Installing tools and dependencies

Create a conda environment called ‘aaftf’ and install several tools needed by the workflow:

conda create -n aaftf "python>=3.6" bbmap trimmomatic bowtie2 bwa pilon sourmash blast minimap2 spades megahit novoplasty biopython -c bioconda

Activate the conda environment:

conda activate aaftf

Install the aaftf pipeline as follows:

python -m pip install git+https://github.com/stajichlab/AAFTF.git

To deactivate the environment do:

2. Running AAFTF pipeline

To run jobs on the HPC, we use PBS Pro submission scripts that will submit jobs to an scheduler that will then send jobs to the queue. Use the PBS Pro script below to run 1) quality trimming and filtering; 2) de novo assembly; and 3) check contaminant sequences using the AAFTF pipeline:

The above template is to run the AAFTF pipeline for the Mort strain, to use it for the Alpine strain we need to modify the following two variables in the above script:

Once change the above variables then you can submit the launch_AAFTF_pipeline.pbs script to the scheduler as follows:

Check the progress of the pipeline:

List of public genomes

https://www.ncbi.nlm.nih.gov/genome/browse/#!/eukaryotes/11236/

Fetch for phospholipase proteins: