Assembly with Flye

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)

ID	Name	Description	Type
long reads	long reads	n/a	File

Name

Description

Type

long reads

n/a

Steps

ID	Name	Description
1	Flye: assembly	toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.8.2+galaxy0
2	Fasta statistics	toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3
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

Outputs

ID	Name	Description	Type
Flye assembly on input dataset(s) (consensus)	Flye assembly on input dataset(s) (consensus)	n/a	File
Flye assembly on input dataset(s) (assembly_graph)	Flye assembly on input dataset(s) (assembly_graph)	n/a	File
Flye assembly on input dataset(s) (Graphical Fragment Assembly)	Flye assembly on input dataset(s) (Graphical Fragment Assembly)	n/a	File
Flye assembly on input dataset(s) (assembly_info)	Flye assembly on input dataset(s) (assembly_info)	n/a	File
Flye assembly on input dataset(s) (log)	Flye assembly on input dataset(s) (log)	n/a	File
_anonymous_output_1	_anonymous_output_1	n/a	File
Bandage Image on input dataset(s): Assembly Graph Image	Bandage Image on input dataset(s): Assembly Graph Image	n/a	File
Quast on input dataset(s): Log	Quast on input dataset(s): Log	n/a	File
Quast on input dataset(s): PDF report	Quast on input dataset(s): PDF report	n/a	File
Quast on input dataset(s): tabular report	Quast on input dataset(s): tabular report	n/a	File
Quast on input dataset(s): HTML report	Quast on input dataset(s): HTML report	n/a	File
Bar chart showing contig sizes	Bar chart showing contig sizes	n/a	File

Assembly with Flye
Version 1