2 - Assembly
Version 1

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.

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

unicycler

Anaconda-Server Badge

spades

Anaconda-Server Badge

bandage

Anaconda-Server Badge

Inputs

ID Name Description Type
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

Steps

ID Name Description
0 Forward reads
1 Reverse reads
2 ONT reads
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

Outputs

ID Name Description Type
assembly_graph assembly_graph n/a tabular
assembly assembly n/a fasta
out_contig_stats out_contig_stats n/a tabular
out_scaffold_stats out_scaffold_stats n/a tabular
out_contigs out_contigs n/a fasta
out_scaffolds out_scaffolds n/a fasta
out_log out_log n/a txt
contig_graph contig_graph n/a txt
scaffold_graph scaffold_graph n/a txt
outfile outfile n/a txt
outfile outfile n/a jpg
outfile outfile n/a jpg
outfile outfile n/a txt
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Views: 281   Downloads: 4

Created: 25th Mar 2020 at 10:02

Last updated: 25th Mar 2020 at 11:23

Last used: 26th Nov 2020 at 14:46

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