snpdists
Tags: snp distance alignment phylogeny core-genome run-scope
Calculate pairwise SNP distances from sequence alignments.
This subworkflow uses snp-dists to compute pairwise SNP distance matrices from multiple sequence alignments. It reads an alignment file (typically a core-genome alignment) and calculates the number of SNP differences between each pair of sequences, producing a distance matrix useful for phylogenetic and epidemiological analyses.
Take
alignment: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
aln | Multiple sequence alignment in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
tsv | Pairwise SNP distance matrix in TSV format |
Module Composition
This subworkflow calls the following modules:
- snpdists - Create a SNP distance matrix from a multiple sequence alignment.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
snp-dists
Seemann T snp-dists - Pairwise SNP distance matrix from a FASTA sequence alignment. (GitHub)