Assess genome quality

Version 1

Assess genome quality; can run alone or as part of a combined workflow for large genome assembly.

• What it does: Assesses the quality of the genome assembly: generate some statistics and determine if expected genes are present; align contigs to a reference genome.
• Inputs: polished assembly; reference_genome.fasta (e.g. of a closely-related species, if available).
• Outputs: Busco table of genes found; Quast HTML report, and link to Icarus contigs browser, showing contigs aligned to a reference genome
• Tools used: Busco, Quast
• Input parameters: None required

Workflow steps:

Polished assembly => Busco

• First: predict genes in the assembly: using Metaeuk
• Second: compare the set of predicted genes to the set of expected genes in a particular lineage. Default setting for lineage: Eukaryota

Polished assembly and a reference genome => Quast

• Contigs/scaffolds file: polished assembly
• Type of assembly: Genome
• Use a reference genome: Yes
• Reference genome: Arabidopsis genome
• Is the genome large (> 100Mbp)? Yes.
• All other settings as defaults, except second last setting: Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?: change to No

Options

Gene prediction:

• Change tool used by Busco to predict genes in the assembly: instead of Metaeuk, use Augustus.
• To do this: select: Use Augustus; Use another predefined species model; then choose from the drop down list.
• Select from a database of trained species models. list here: https://github.com/Gaius-Augustus/Augustus/tree/master/config/species
• Note: if using Augustus: it may fail if the input assembly is too small (e.g. a test-size data assembly). It can't do the training part properly.

Compare genes found to other lineage:

• Busco has databases of lineages and their expected genes. Option to change lineage.
• Not all lineages are available - there is a mix of broader and narrower lineages. - list of lineages here: https://busco.ezlab.org/list_of_lineages.html.
• To see the groups in taxonomic hierarchies: Eukaryotes: https://busco.ezlab.org/frames/euka.htm
• For example, if you have a plant species from Fabales, you could set that as the lineage.
• The narrower the taxonomic group, the more total genes are expected.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)