Assembly with Flye
Version 1

Workflow Type: Galaxy

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)

Inputs

ID Name Description Type
long reads long reads n/a n/a
in in runtime parameter for tool Quast n/a

Steps

ID Name Description
0 long reads
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
consensus consensus n/a
assembly_graph assembly_graph n/a
assembly_gfa assembly_gfa n/a
assembly_info assembly_info n/a
flye_log flye_log n/a
stats stats n/a
outfile outfile n/a
quast_tabular quast_tabular n/a
report_html report_html n/a
report_pdf report_pdf n/a
log log n/a
out_file1 out_file1 n/a

Version History

Version 1 (earliest) Created 8th Nov 2021 at 05:07 by Anna Syme

Added/updated 2 files


Open master 9541ba8
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Citation
Syme, A. (2021). Assembly with Flye. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.225.1
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Views: 1271   Downloads: 4

Created: 8th Nov 2021 at 05:07

Last updated: 9th Nov 2021 at 01:11

Last used: 2nd Dec 2022 at 12:45

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