Reproducibility

In order to recreate the bioinformatics and analyses completed in the Manuscript Brazeau & Levinson et al. 2019, you will need to run the two "pipelines" below:

Referent Guided Alignments/WGS

1. Alignment (wgs_pe_improved)
2. Quality Control/Quality Analysis (qc)
3. Short variant Calling (gatk)
4. Run Structural Variant Discovery (smoothlumpy)
5. Variant Filtration (make_regions)

de novo Assembly/CGE pipeline

1. Run CGE submodules (except plasmidfinder) (CGEtools_noplasmidfinder)
2. Run Plasmidfinder (plasmidfinder_tools)

Dependencies

• bwa-mem version 0.7.17
• cutadapt version 2.3
• samblaster version 0.1.24
• samtools version 1.9
• Picard Tools version 2.20.3
• bedtools version 2.28.0
• GATK version 4.0.3.0
• GATK version 3.8.0 (For the CallableLoci and VariantAnnotator tools)
• snpEFF version 4.3t
• smoove version 0.2.3
• bcftools version 1.9
• CGE Tools Pipeline Docker Image
• PlasmidFinder