Combined workflow for large genome assembly

The tutorial document for this workflow is here: https://doi.org/10.5281/zenodo.5655813

What it does: A workflow for genome assembly, containing subworkflows:

• Data QC
• Kmer counting
• Trim and filter reads
• Assembly with Flye
• Assembly polishing
• Assess genome quality

Inputs:

• long reads and short reads in fastq format
• reference genome for Quast

Outputs:

• Data information - QC, kmers
• Filtered, trimmed reads
• Genome assembly, assembly graph, stats
• Polished assembly, stats
• Quality metrics - Busco, Quast

Options

• Omit some steps - e.g. Data QC and kmer counting
• Replace a module with one using a different tool - e.g. change assembly tool

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)