Genome-assessment-post-assembly

v2.0.5 (latest)

• v2.0.5 (latest)
  
• v2.0.4
  
• v2.0.2
  
• v1.1.0
  
• v1.0.0 (earliest)
  

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics. Updates November 2023.

• Inputs: reads as fastqsanger.gz (not fastq.gz), and assembly.fasta. (To change format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz).
• New default settings for BUSCO: lineage = eukaryota; for Quast: lineage = eukaryotes, genome = large.
• Reports assembly stats into a table called metrics.tsv, including selected metrics from Fasta Stats, and read coverage; reports BUSCO versions and dependencies; and displays these tables in the workflow report.
• Note: a known bug is that sometimes the workflow report text resets to default text.
• To restore: open the workflow in Galaxy for editing.
• Click on the "Edit Report" icon
• Copy and paste the following text into the workflow report, then exit and save.

# Workflow Execution Report

Workflow name: Genome assessment post assembly

## Genome assembly metrics

Selected statistics from the workflow outputs. Additional metrics are available in other outputs in the history.

```galaxy
history_dataset_display(output="Genome assembly metrics")
```

## Software

Busco version and dependencies:

```galaxy
history_dataset_display(output="Busco and dependencies version")
```

## Galaxy Australia

Thanks for using Galaxy! When you use Galaxy Australia to support your publication or project, please acknowledge its use with the following statement: "This work is supported by Galaxy Australia, a service provided by the Australian Biocommons and its partners. The service receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons (https://doi.org/10.47486/PL105), as well as The University of Melbourne and Queensland Government RICF funding."