2 - Assembly
Version 1

Workflow Type: Galaxy

Assembly of SARS-CoV-2 from pre-processed reads

Live Resources

usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be

Galaxy workflow Galaxy workflow Galaxy workflow Galaxy workflow

Galaxy history Galaxy history Galaxy history Galaxy history

What's the point?

Use a combination of Illumina and Oxford Nanopore reads to produce SARS-CoV-2 genome assembly.


We use Illumina and Oxford Nanopore reads that were pre-processed to remove human-derived sequences. We use two assembly tools: spades and unicycler. While spades is a tool fully dedicated to assembly, unicycler is a "wrapper" that combines multiple existing tools. It uses spades as an engine for short read assembly while utilizing mimiasm and racon for assembly of long noisy reads.

In addition to assemblies (actual sequences) the two tools produce assembly graphs that can be used for visualization of assembly with bandage.


Filtered Illumina and Oxford Nanopore reads produced during the pre-processing step are used as inputs to the assembly tools.


Each tool produces assembly (contigs) and assembly graph representations. The largest contigs generated by unicycler and spades were 29,781 and 29,907 nts, respectively, and had 100% identity over their entire length.

The following figures show visualizations of assembly graphs produced with spades and unicycler. The complexity of the graphs is not surprising given the metagenomic nature of the underlying samples.

Assembly graphs for Unicycler (A) and SPAdes (B)

A. Unicycler assembly graph

B. SPAdes assembly graph

History and workflow

A Galaxy workspace (history) containing the most current analysis can be imported from here.

The publicly accessible workflow can be downloaded and installed on any Galaxy instance. It contains version information for all tools used in this analysis.


Tools used in this analysis are also available from BioConda:

Name Link

unicycler Anaconda-Server Badge

spades Anaconda-Server Badge

bandage Anaconda-Server Badge


ID Name Description Type
Forward reads Forward reads n/a
  • File
ONT reads ONT reads n/a
  • File
Reverse reads Reverse reads n/a
  • File


ID Name Description
3 Create assemblies with Unicycler toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/
4 SPAdes toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1
5 Bandage Info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
6 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
7 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
8 Bandage Info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1

Version History

Version 1 (earliest) Created 25th Mar 2020 at 10:02 by Finn Bacall

Added/updated 6 files

Open master 23e40c4
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Views: 1580   Downloads: 160

Created: 25th Mar 2020 at 10:02

Last updated: 25th Mar 2020 at 11:23

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