snpdists

Tags: snp distance matrix alignment phylogeny run-scope

Create a SNP distance matrix from a multiple sequence alignment.

Uses snp-dists to read a FASTA alignment and compute a pairwise SNP distance matrix between all sequences.

Inputs

record (
    meta: Record,
    aln: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
aln	Path	Multiple sequence alignment in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Pairwise SNP distance matrix in TSV format
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

SNP-Dists Parameters

Parameter	Type	Default	Description
--snpdists_a	boolean	false	Count all differences not just [AGTC]

Used By

Subworkflows

• snpdists - Calculate pairwise SNP distances from sequence alignments.

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)

Source

View source on GitHub

Version

SNPDISTS:
    - snp-dists: 1.2.0