Workflows

What is a Workflow?
3 Workflows visible to you, out of a total of 3

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

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Anton Nekrutenko

Stable

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 | ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Anton Nekrutenko

Stable

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 ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Anton Nekrutenko

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