COVID-19 Biohackathon

Overview
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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

Finn Bacall

Teams: IBISBA Workflows, nf-core viralrecon, Testing

Organizations: The University of Manchester

Frederik Coppens

Teams: GalaxyProject SARS-CoV-2, usegalaxy.be workflows

Organizations: ELIXIR Belgium

https://orcid.org/0000-0001-6565-5145

Flora D'Anna

Teams: GalaxyProject SARS-CoV-2

Organizations: ELIXIR Belgium

https://orcid.org/0000-0003-4665-6673

Bert Droesbeke

Teams: GalaxyProject SARS-CoV-2, Galaxy Training Network

Organizations: ELIXIR Belgium

https://orcid.org/0000-0003-0522-5674

Dan Fornika

Teams: GalaxyProject SARS-CoV-2

Organizations: BC Centre for Disease Control

https://orcid.org/0000-0002-6178-3585

Expertise: Bioinformatics, Data Management, Molecular Biology

Tools: Databases, PCR, Workflows, Web services

View all 21 items

V-Pipe

No description specified

Space: COVID-19 Biohackathon

Public web page: Not specified

Organisms: Homo sapiens, SARS-CoV-2

GalaxyProject 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

Test team

No description specified

Space: COVID-19 Biohackathon

Public web page: Not specified

Organisms: Not specified

CWL workflow SARS-CoV-2

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

nf-core viralrecon

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

View all 7 items

Albert-Ludwigs-Universität Freiburg

Country: Germany

City: Not specified

Web page: Not specified

Australian BioCommons

Country: Australia

City: Not specified

Web page: Not specified

Barcelona Supercomputing Center (BSC-CNS)

Country: Spain

City: Barcelona

Web page: https://www.bsc.es/

BC Centre for Disease Control

Country: Canada

City: Not specified

Web page: Not specified

Earlham Institute

Country: United Kingdom

City: Not specified

Web page: https://www.earlham.ac.uk/

View all 12 items

Standard Operating Protocol for SNPs and INDELs detection using GATK4.

CWL workflow SARS-CoV-2

No description specified

Creator: Ambarish Kumar

Submitter: Ambarish Kumar

External Link

Created: 18th Jun 2020 at 05:12

Standard Operating Protocol for SNPs and INDELs detection using SAMTools.

CWL workflow SARS-CoV-2

Detects SNPs and short INDELs.

Creator: Ambarish Kumar

Submitter: Ambarish Kumar

External Link

Created: 18th Jun 2020 at 05:09

Standard Operating Protocol for SNPs and INDELs detection using VARSCAN2.

CWL workflow SARS-CoV-2

Detects SNPs and short INDELs.

Creator: Ambarish Kumar

Submitter: Ambarish Kumar

External Link

Created: 18th Jun 2020 at 05:01

INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

InSaFLU

Abstract (Expand)

Background A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized …d by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. Results We developed and implemented INSaFLU (“INSide the FLU”), which is the first influenza-oriented bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line “genetic requests” for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants’ annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform multi-step software intensive analyses in a user-friendly manner without previous advanced training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. This platform additionally flags samples as “putative mixed infections” if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional “consensus-based” influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. Conclusions In summary, INSaFLU supplies public health laboratories and influenza researchers with an open “one size fits all” framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus.

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)

Created: 8th Apr 2020 at 11:56, Last updated: 8th Apr 2020 at 11:57

SARS-CoV-2 Data Analysis and Monitoring with Galaxy

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

Created: 1st Dec 2021 at 18:06

V-pipe (main multi-virus version)

V-Pipe

Stable

...

Type: Snakemake

Creators: Ivan Topolsky, Kim Philipp Jablonski

Submitter: Ivan Topolsky

Created: 30th Mar 2022 at 17:50

(old) SARS-COV2 version of the V-Pipe workflow

V-Pipe

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

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