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Eyre

It is a similar workflow as Nullarbor, but it only runs isolate specific analysis. No phylogenetic tree and pangenome analysis will be generated. A snakemake workflow that process fastq files of bacterial pathogens to produce:

  1. Sequencing yield (fq),
  2. Species identification (Kraken2),
  3. de novo assemblies (shovill) and their qc (fa)
  4. Subtyping (MLST)
  5. Antimicrobial resistance profile (abricate)

Requirements

It is practically a snakemake workflow with all other softwares from Nullarbor.

  1. Nullarbor

It is best to install Nullarbor using conda.

$ conda create -n eyre nullarbor
  1. Snakemake

The snakemake software should be added to the Nullarbor conda environment

$ conda activate eyre
$ conda install snakemake
  1. Git clone the eyre repository
$ git clone https://github.com/lexleong/eyre.git
  1. Download Kraken2 database

Modification on the Snakefile is required to direct the pipeline script to the directory path containing kraken2 database files (hash.k2d, taxo.k2d, and opts.k2d).

Workflow

  1. Modify the sequencing submission sheet as per the SampleSheet.csv template

  2. Run the bcl2eyre.sh script

$ bcl2eyre.sh [dir]/SampleSheet.csv

Etymology

The Nullarbor is a huge treeless plain that spans the area between South Australia and Western Australia. If one were to travel from Adelaide to Nullarbor, one will have to go through Eyre Peninsula. So a South Australian public health microbiologist has to perform the Eyre pipeline prior to the Nullarbor pipeline for their bacterial WGS.

Disclaimer

This workflow is specific to working in slurm and conda environments. It is used mainly by SA Pathology MID PHL for downstream processing of bacterial whole genome sequencing output.