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
- 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
- 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)
|long reads||long reads||n/a||n/a|
|in||in||runtime parameter for tool Quast||n/a|
|3||Bandage image: Flye assembly||toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3|
|4||Quast genome report||toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy1|
|5||Bar chart: show contig sizes||barchart_gnuplot|
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Created: 8th Nov 2021 at 05:07
Last updated: 9th Nov 2021 at 01:11
Last used: 2nd Dec 2022 at 12:45