This team and associated Galaxy workflows are maintained by the European Galaxy Team.

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Workflow for variant analysis against a reference genome in GenBank format

Generic consensus building

This workflow generates consensus sequences using a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

• A collection of VCF files

The workflow produces a single output:

• Consensus sequence for each input VCF file

The workflow can be accessed at usegalaxy.org

Generic variation analysis reporting

This workflow generates reports from a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

• A collection of VCF files

The workflow produces two outputs (format description below):

1. A list of variants grouped by Sample
2. A list of variants grouped by Variant

Here is example of output by sample. In this table all varinats in all samples are epxlicitrly listed:

| Sample | ...

Generic variant calling

A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:

• A genbank file with the reference genomes
• A collection of paired fastqsanger files

The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.

Workflow can be accessed ...