Infer phylogeny between genomic sequences¶
Compare sequences from the reference FASTA file and visualise their relationship in form of phylogenetic tree and interactive multiple alignment.
Purpose¶
- Assess relationship and similarity between genomic sequences
Generated outputs¶
- Phylogenetic tree with distances between genomic sequences
- Interactive visualization of multiple alignment of reference sequences
Example¶
How to run example:
cd /usr/local/snakelines/example/fasta_processing
snakemake \
--snakefile ../../snakelines.snake \
--configfile config_infer_phylogeny.yaml \
--use-conda
Example configuration:
sequencing: paired_end
samples: # List of sample categories to be analysed
- reference: lacto_supplied # Reference genome for reads in the category (reference/lacto_supplied/lacto_supplied.fa)
report_dir: report/public/01-phylogeny # Generated reports and essential output files would be stored there
reference: # Prepare and analyse reference sequences
alignment: # Multiple alignment of reference sequences
method: mafft # Supported values: mafft
phylogeny: # Assess phylogenetic relationship between sequences
method: iqtree # Supported values: iqtree
model: GTR+I+G4 # Model to use for phylo tree generation - see iqtree documentation
report: # Visually assess relationship between reference sequences
phylogenetic_tree: # Visual inspection of distances between sequences in tree graph structure
method: phylo # Supported values: phylo
comparison: # Interactive HTML visualization of multiple alignment
method: msaviewer # Supported values: msaviewer
Planned improvements¶
- SVG figure size should be scaled with the number of the sequences
Included pipelines¶
- None