COVID-19 Biohackathon

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org

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.

CWL workflows related to virus genomics with focus on 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.

Nextflow pipelines for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

Detects SNPs and short INDELs.

Detects SNPs and short INDELs.

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 ...

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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.

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.

Detects SNPs and INDELs.

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 ...

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 ...

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/

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/

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/

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/