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 ...

Taxonomy Assignment with QIIME2

This workflow performs taxonomic assignment for an input OTU/ASV (Operating Taxonomic Unit/Amplicon Sequence Variant) Feature Table and set of amplicon Representative Sequences using QIIME2. The workflow creates and trains a QIIME2 classifier for an input reference taxonomic database (e.g. HOMD, SILVA, PR2, UNITE) and uses the trained classifier to assign taxonomy ...