Genome Lab demo: Fusarium graminearum genome assembly and annotation walkthrough (Galaxy Australia history)

Galaxy history exported as an RO-Crate archive, supporting the paper The Genome Lab: designing a simpler interface for genome assembly and annotation (Galaxy Australia). The history is also available in Galaxy Australia at https://genome.usegalaxy.org.au/u/gtntesting/h/genome-lab-demo.

It contains a ten-step walkthrough of genome assembly and annotation carried out through the Genome Lab (https://genome.usegalaxy.org.au): read quality with NanoPlot, subsampling with seqtk, the Flye assembly workflow (Flye, Fasta statistics, Bandage, Quast and a contig size chart), completeness assessment with Busco, gene prediction with Helixer, and visualisation in JBrowse. All outputs, tool parameters and tool versions are included.

Input data. The walkthrough starts from public Oxford Nanopore reads for Fusarium graminearum strain FG-12, NCBI SRA run SRR15058295, BioProject PRJNA743144 (Hao et al. 2021, https://doi.org/10.3390/jof7090699). Because these reads are already archived at NCBI, the raw read file (8.2 GB) is not duplicated in this archive; the subsampled reads used for assembly are included. To bring the raw reads into Galaxy, run the tool Faster Download and Extract Reads in FASTQ format from NCBI SRA (fasterq-dump) with the accession SRR15058295, or download the run from https://www.ncbi.nlm.nih.gov/sra/SRR15058295 and upload it with the Galaxy Upload tool.

The archive (Genome-Lab-demo.rocrate.zip) can be imported into any Galaxy server via Import History from file, or opened as a standard RO-Crate.