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, Testing, Defragmentation TS, EuroScienceGateway, ELIXIR Training
Organizations: The University of Manchester
Teams: GalaxyProject SARS-CoV-2, usegalaxy.be workflows, EuroScienceGateway
Organizations: ELIXIR Belgium, VIB
https://orcid.org/0000-0001-6565-5145
Teams: GalaxyProject SARS-CoV-2, Galaxy Training Network
Organizations: ELIXIR Belgium
https://orcid.org/0000-0003-0522-5674
Teams: GalaxyProject SARS-CoV-2
Organizations: BC Centre for Disease Control
https://orcid.org/0000-0002-6178-3585
Teams: usegalaxy-eu, GalaxyProject SARS-CoV-2
Organizations: European Galaxy Team
https://orcid.org/0000-0002-9464-6640
Teams: usegalaxy-eu, Galaxy Training Network, GalaxyProject SARS-CoV-2
Organizations: Galaxy
https://orcid.org/0000-0002-5987-8032
Teams: GalaxyProject SARS-CoV-2, nf-core viralrecon, EOSC-Life - Demonstrator 7: Rare Diseases, iPC: individualizedPaediatricCure, EJPRD WP13 case-studies workflows, TransBioNet, OpenEBench, ELIXIR Proteomics
Organizations: Barcelona Supercomputing Center (BSC-CNS), ELIXIR
https://orcid.org/0000-0003-4929-1219
Computer Engineer in Barcelona Supercomputing Center (BSC)
Teams: IBISBA Workflows, GalaxyProject SARS-CoV-2, BioBB Building Blocks, Common Workflow Language (CWL) community, BioExcel Best Practice Guides, Specimen Data Refinery, FAIR Computational Workflows, Vertebrate Genomes Pipelines in Galaxy, TRE-FX, EuroScienceGateway, Biodiversity Genomics Europe (general), BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection, BY-COVID (general), BioDT additional pipelines, BioDT Use Case 4.1.1.1 Biodiversity dynamics, BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats, BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security, BioDT Use Case 4.1.3.1 Invasive species, BioDT Use Case 4.1.3.2 Endangered species, BioDT Use Case 4.1.4.1 Disease outbreaks, BioDT Use Case 4.1.4.2 Pollinators, BioDT Use Case 4.1.1.2 Ecosystem services, ELIXIR Training, ELIXIR Tools platform
Organizations: The University of Manchester, ELIXIR-UK
https://orcid.org/0000-0001-9842-9718
Teams: GalaxyProject SARS-CoV-2
Organizations: Earlham Institute
https://orcid.org/0000-0003-3627-5340
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
INSaFLU (“INSide the FLU”) is an influenza-oriented bioinformatics free web-based platform for an effective and timely whole-genome-sequencing-based influenza laboratory surveillance.
Space: COVID-19 Biohackathon
Public web page: https://github.com/INSaFLU/INSaFLU
Space: COVID-19 Biohackathon
Public web page: Not specified
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
Nextflow pipelines for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Space: COVID-19 Biohackathon
Public web page: https://github.com/connor-lab/ncov2019-artic-nf
Country: Not specified
City: Not specified
Web page: Not specified
Country: Not specified
City: Not specified
Web page: Not specified
Creator: Ambarish Kumar
Submitter: Ambarish Kumar
External LinkDetects SNPs and short INDELs.
Creator: Ambarish Kumar
Submitter: Ambarish Kumar
Detects SNPs and short INDELs.
Creator: Ambarish Kumar
Submitter: Ambarish Kumar
Abstract (Expand)
Authors: Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes
Date Published: 1st Dec 2018
Publication Type: InProceedings
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
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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.
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
Analysis of variation within individual COVID-19 samples using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation This worklow was ported into CWL from a Galaxy Workflow ( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using SAMTools.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Detects SNPs and INDELs using VARSCAN2.
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using VARSCAN.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible. Pipeline Steps
Step Main program/s
Trimming, combining of read-pairs per sample and QC Skewer, FastQC
Decontamination ...
Type: Nextflow
Creator: Andreas Wilm and October SESSIONS and Paola Florez DE SESSIONS and ZHU Yuan and Shuzhen SIM and CHU Wenhan Collins
Submitter: Laura Rodriguez-Navas
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. This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international ...
Type: Nextflow
Creator: Sarai Varona and Miguel Juliá and Sara Monzon and Alexander Peltzer and Alison Meynert and Edgar Garriga Nogales and Erik Garrison and Gisela Gabernet and Harshil Patel and Joao Curado and Jose Espinosa-Carrasco and Katrin Sameith and Marta Pozuelo and Maxime Garcia and Michael Heuer and Phil Ewels and Simon Heumos and Stephen Kelly and Thanh Le Viet and Isabel Cuesta
Submitter: Hervé Ménager
This workflow is used for the virtual screening of the SARS-CoV-2 main protease (de.NBI-cloud, STFC). It includes Charge enumeration, Generation of 3D conformations, Preparation of active site for docking using rDock, Docking, Scoring and Selection of compounds available. More info can be found at https://covid19.galaxyproject.org/cheminformatics/
Type: Galaxy
Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft
Submitter: Bert Droesbeke
This workflow combines SDF files from all fragments into a single dataset and filters to include only the lowest (best) scoring pose for each compound. This file of optimal poses for all ligands is used to compare to a database of Enamine and Chemspace compounds to select the best scoring 500 matches. More info can be found at https://covid19.galaxyproject.org/cheminformatics/
Type: Galaxy
Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft
Submitter: Bert Droesbeke
This workflow generates binding scores that correlate well with binding affinities using an additional tool TransFS, developed at Oxford University. More info can be found at https://covid19.galaxyproject.org/cheminformatics/
Type: Galaxy
Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft
Submitter: Bert Droesbeke
This workflow generates binding scores that correlate well with binding affinities using an additional tool SuCOS Max, developed at Oxford University. More info can be found at https://covid19.galaxyproject.org/cheminformatics/
Type: Galaxy
Creator: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, Jack Scantlebury, Susan Leung, Frank von Delft
Submitter: Bert Droesbeke
