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94 Workflows visible to you, out of a total of 126

Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: Assembly

Type: Common Workflow Language

Creator: Ignacio Eguinoa

Submitter: Ignacio Eguinoa

Abstract CWL generated from Galaxy workflow file: COVID-19: read pre-processing from SRA data

Type: Common Workflow Language

Creator: Ignacio Eguinoa

Submitter: Ignacio Eguinoa

Evolutionary Analysis

Live Resources

usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be

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 ...

Type: Galaxy

Creator: Finn Bacall

Submitter: Finn Bacall

Analysis of S-protein polymorphism

Live Resources

usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be

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 ...

Type: Galaxy

Creator: Finn Bacall

Submitter: Finn Bacall

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 ...

Type: Galaxy

Creator: Finn Bacall

Submitter: Finn Bacall

Dating the most recent common ancestor (MRCA) of SARS-CoV-2

Live Resources

usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be

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 ...

Type: Galaxy

Creator: Finn Bacall

Submitter: Finn Bacall

Assembly of SARS-CoV-2 from pre-processed reads

Live Resources

usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be

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 ...

Type: Galaxy

Creator: Finn Bacall

Submitter: Finn Bacall

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