Workflows

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

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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

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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

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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 ...

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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What's the point?

Assess quality of reads, remove adapters and remove reads mapping to human genome.

The outline

Illumina and Oxford nanopore reads are pulled from the ...

BROAD Best Practices Somatic CNV Panel is used for creating a panel of normals (PON) given a set of normal samples.

Common Use Cases

For CNV discovery, the PON is created by running the initial coverage collection tools individually on a set of normal samples and combining the resulting copy ratio data using a dedicated PON creation tool [1]. This produces a binary file that can be used as a PON. It is very important to use normal samples that are as technically similar as possible to the ...