Assembly of SARS-CoV-2 from pre-processed reads
Live Resources
usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be
What's the point?
Use a combination of Illumina and Oxford Nanopore reads to produce SARS-CoV-2 genome assembly.
Outline
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
.
Inputs
Filtered Illumina and Oxford Nanopore reads produced during the pre-processing step are used as inputs to the assembly tools.
Outputs
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.
BioConda
Tools used in this analysis are also available from BioConda:
Name Link
Inputs
ID | Name | Description | Type |
---|---|---|---|
Forward reads | Forward reads | n/a |
|
ONT reads | ONT reads | n/a |
|
Reverse reads | Reverse reads | n/a |
|
Steps
ID | Name | Description |
---|---|---|
3 | Create assemblies with Unicycler | toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0 |
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
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Submitter
Views: 1731 Downloads: 224
Created: 25th Mar 2020 at 10:02
Last updated: 25th Mar 2020 at 11:23
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