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Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: Assembly
DownloadAbstract CWL generated from Galaxy workflow file: COVID-19: read pre-processing from SRA data
Evolutionary Analysis
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What's the point?
Wu et al. showed recombination between COVID-19 and bat coronaviruses located within the S-gene. We want to confirm this observation and provide a publicly accessible workflow for recombination detection.
In previous coronavirus outbreaks (SARS), retrospective analyses determined that adaptive substitutions might have occurred in the S-protein Zhang et al., e.g., related to ACE2 receptor ...
Analysis of S-protein polymorphism
Live Resources
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What's the point?
In the previous portion of this study we found a non-synonymous polymorphism within the S-gene. In this section we are trying to interpret its possible effect.
Outline
Obtain coding sequences of S proteins from a diverse group of coronaviruses. Generate amino acid alignment to assess conservation of the polymorphic location.
Input
Downloaded CDS sequences of coronavirus ...
Analysis of variation within individual COVID-19 samples | March 20 2020
What's the point?
The absolute majority of SARS-COV-2 data is in the form of assembled genomic sequences. This is unfortunate because any variation that exists within individual samples is obliterated--converted to the most frequent base--during the assembly process. However, knowing underlying evolutionary dynamics is critical for tracing evolution of the virus as it allows identification of genomic regions under different ...
Dating the most recent common ancestor (MRCA) of SARS-CoV-2
Live Resources
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What's the point?
To estimate the time of COVID-19 emergence we use simple root-to-tip regression (Korber et al. 2000; more complex and powerful phylodynamics methods could certainly be used, but for this data with very low levels of sequence divergence, simpler and faster methods suffice). From the set of all COVID-19 sequences available as of Feb 16, 2020 we obtain ...
Assembly of SARS-CoV-2 from pre-processed reads
Live Resources
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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 ...
