squirrel-nf

Workflow to run squirrel through a GUI

Some QUIck Rearranging to Resolve Evolutionary Links

A full walkthrough of this workflow can be found here

Squirrel allows the following analyses of MPXV Clade I or Clade II sequences:

1. Generate an alignment
2. Run basic sequence QC on the alignment looking for standard errors arising from consensus building pipelines or low sequencing depth
3. Build a phylogenetic tree
4. Build a phylogenetic tree and run additional sequence QC based on this phylogeny

When QC is performed, the pipeline produces a CSV file of suggested sites which are likely to be errors and should be masked. This file can be provided to a rerun of squirrel to improve the alignment.

1. Generate a quick MPXV alignment

Provide a FASTA file of consensus sequences and select the appropriate clade from the drop down menu.

2. Run basic sequence QC

If you check the seq_qc option, it will run additional QC

3. Build a phylogenetic tree

If you check the run_phylo option, it will construct a tree using IQtree. You will need to specify the outgroups (which need to be in the input FASTA file) and these are used to help root the phylogeny so that ancestral reconstruction can be performed in the appropriate direction.

4. Additional phylogenetic QC

If you check both the run_phylo and seq_qc options, and additional step is performed to generate a more informed mask file.

More information

More information on the input parameters and methods can be found on the main page for squirrel.