COVID-19 Biohackathon
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
Organizations: The University of Manchester
Teams: GalaxyProject SARS-CoV-2, Galaxy Training Network
Organizations: ELIXIR Belgium
https://orcid.org/0000-0003-0522-5674
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
Space: COVID-19 Biohackathon
Public web page: 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
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
Space: COVID-19 Biohackathon
Public web page: Not specified
External Link
Abstract (Expand)
Authors: Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes
Date Published: 1st Dec 2018
Publication Type: InProceedings
Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).
DownloadAlignment, assembly RNASEQ reads and annotation of generated transcripts.
Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.
Alignment, assembly and annotation of generated transcripts from RNASEQ reads.
Virus genome assembly with Unicycler and Spades,
The 2 assemblers works in parallel. The graph visualization is made with Bandage.
workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl
Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png
