Finn Bacall
SEEK ID: https://dev.workflowhub.eu/people/1
Location:
United Kingdom
Expertise: Not specified
Tools: Not specified
ORCID: Not specified
Team roles
Project administrator
Their tagsRelated items
Concerning the administration of the Workflow Hub.
Space: This Team is not associated with a Space
Public web page: Not specified
Start date: 28th Feb 2020
A project for miscellaneous testing of Workflow Hub.
Space: General
Public web page: Not specified
Initial analysis of COVID-19 data using Galaxy, BioConda and public research infrastructures
Space: This Team is not associated with a Space
Public web page: https://covid19.galaxyproject.org
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Space: This Team is not associated with a Space
Public web page: https://nf-co.re/
MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data.
Space: This Team is not associated with a Space
Public web page: https://www.ebi.ac.uk/metagenomics/
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.
Live Resources
| usegalaxy.org | usegalaxy.eu | usegalaxy.org.au | usegalaxy.be |
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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 ...
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 ...
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 ...
nf-core workflows
