Assembly with Flye; can run alone or as part of a combined workflow for large genome assembly.

• What it does: Assembles long reads with the tool Flye
• Inputs: long reads (may be raw, or filtered, and/or corrected); fastq.gz format
• Outputs: Flye assembly fasta; Fasta stats on assembly.fasta; Assembly graph image from Bandage; Bar chart of contig sizes; Quast reports of genome assembly
• Tools used: Flye, Fasta statistics, Bandage, Bar chart, Quast
• Input parameters: None required, but recommend setting assembly mode to match input sequence type

Workflow steps:

• Long reads are assembled with Flye, using default tool settings. Note: the default setting for read type ("mode") is nanopore raw. Change this at runtime if required.
• Statistics are computed from the assembly.fasta file output, using Fasta Statistics and Quast (is genome large: Yes; distinguish contigs with more that 50% unaligned bases: no)
• The graphical fragment assembly file is visualized with the tool Bandage.
• Assembly information sent to bar chart to visualize contig sizes

Options

• See other Flye options.
• Use a different assembler (in a different workflow).
• Bandage image options - change size (max size is 32767), labels - add (e.g. node lengths). You can also install Bandage on your own computer and donwload the "graphical fragment assembly" file to view in greater detail.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)