MPXV (Mpox) Phylogenetic Analysis with Squirrel
Description
Galaxy workflow to perform MPXV phylogenetic reconstruction using the Squirrel (Some QUIck Reconstruction to Resolve Evolutionary Links) Galaxy tools, Squirrel QC and Squirrel Phylo. The workflow also performs masking (using the squirrel tool) of SNPs.
Galaxy Squirrel tools:
Squirrel QC: The quality control (QC) mode of Squirrel that can run QC on the alignment and flag certain sites ...
Viral Amplicon Analysis Pipeline for ONT Data
Description
Galaxy workflow for processing viral amplicon datasets, such as MPXV (Mpox), sequenced using the Oxford Nanopore Technologies (ONT) platform. The workflow uses the latest Fieldbioinformatics Artic Minion pipeline that uses the clair3 variant caller.
The ARTIC minion is a pipeline for working with viral nanopore sequencing data, generated from tiling amplicon schemes. It is designed ...
Tests 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 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 ...
