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- Name of the application: Adapter removal hello world
- Name of the application: Mapping and bam sorting goodbye world
1. Name of the application: Adapter removal hello world 2. Name of the application: Mapping and bam sorting goodbye world
Preprocessing of raw SARS-CoV-2 reads
The raw reads available so far are generated from bronchoalveolar lavage fluid (BALF) and are metagenomic in nature: they contain human reads, reads from potential bacterial co-infections as well as true COVID-19 reads.
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Evolutionary Analysis
Live Resources
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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
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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 ...
