Generic variation analysis on WGS PE data
This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff. The reference genome can be provided as a GenBank file.
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):
- A list of variants grouped by Sample
- 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 ...