Assembly of SARS-CoV-2 from pre-processed reads
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 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
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
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
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
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:
|lr_align||lr_align||runtime parameter for tool Create assemblies with Unicycler||n/a|
|rotation||rotation||runtime parameter for tool Create assemblies with Unicycler||n/a|
|3||Create assemblies with Unicycler||toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0|
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Created: 25th Mar 2020 at 10:02
Last updated: 25th Mar 2020 at 11:23
Last used: 26th Nov 2020 at 14:46