The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone that joins the programme.
Web page: https://github.com/virtual-biohackathons/covid-19-bh20
Funding details:ELIXIR Europe and Galaxy have kindly agreed to provide computing resources
Slack has kindly provided the full Slack version free of charge for up to 90 days.
Related items
Teams: IBISBA Workflows, nf-core viralrecon, Testing
Organizations: The University of Manchester
Teams: GalaxyProject SARS-CoV-2, usegalaxy.be workflows
Organizations: ELIXIR Belgium

Teams: GalaxyProject SARS-CoV-2, Galaxy Training Network
Organizations: ELIXIR Belgium

Teams: GalaxyProject SARS-CoV-2
Organizations: BC Centre for Disease Control

Expertise: Bioinformatics, Data Management, Molecular Biology
Tools: Databases, PCR, Workflows, Web services
Space: COVID-19 Biohackathon
Public web page: Not specified
Organisms: Homo sapiens, SARS-CoV-2
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
Organisms: Homo sapiens, SARS-CoV-2
Space: COVID-19 Biohackathon
Public web page: Not specified
Organisms: Not specified
CWL workflows related to virus genomics with focus on SARS-CoV-2.
Space: COVID-19 Biohackathon
Public web page: https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2
Organisms: Homo sapiens, SARS-CoV-2
nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calling for viral samples. The pipeline currently supports metagenomics and amplicon sequencing data derived from the Illumina sequencing platform.
Space: COVID-19 Biohackathon
Public web page: https://github.com/nf-core/viralrecon
Organisms: Homo sapiens, SARS-CoV-2
Abstract (Expand)
Authors: Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes
Date Published: 1st Dec 2018
Publication Type: InProceedings
DOI: 10.1186/s13073-018-0555-0
Citation: Genome Med 10(1)
The goal of this workshop is to build capacity in SARS-CoV-2 data analysis and data management, including data submission to ENA. After the workshop, all participants will be able to upload viral sequencing data, call all variants, create a variety of reports and create consensus alignments.
It will be a 4-day event introducing scalable and reproducible SARS-CoV-2 data analysis with Galaxy. The sessions will be pre-recorded and provided in advance. During the workshop, there will be live support ...
Start Date: 9th Aug 2021
End Date: 12th Aug 2021
Event Website: https://galaxyproject.eu/event/2021-06-21-sars-cov-2-data-analysis-monitoring-training/
Country: Not specified
City: Virtual
A version of V-pipe (analysis of next generation sequencing (NGS) data from viral pathogens) specifically adapted to analyze high-throughput sequencing data of SARS-CoV-2.
Type: Snakemake
Creators: Ivan Topolsky, Susana Posada Céspedes, Niko Beerenwinkel,
Submitter: Hervé Ménager
Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).
Alignment, assembly RNASEQ reads and annotation of generated transcripts.
Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.