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pairsnp-rs

CI Crates.io Version

A fast Rust implementation for calculating pairwise SNP distance matrices from multiple sequence alignments. Inspired by https://github.com/gtonkinhill/pairsnp-cpp.

Installation

cargo install pairsnp-rs

Input

The input file should be a multiple sequence alignment in FASTA format. Both regular and gzipped files are supported. IUPAC ambiguity codes are handled correctly.

Output

The output is a pairwise SNP distance matrix. By default this is written to stdout in TSV format, but can be redirected to a file with -o or switched to CSV with -c. A sparse output mode (-s) is also available, optionally filtered by a distance threshold (-d).

Usage

pairsnp-rs -i input.fasta > output.txt

Use multiple threads for large alignments:

pairsnp-rs -i input.fasta -t 8 -o output.tsv

For more information, run pairsnp-rs --help.

$ pairsnp-rs --help
Calculate pairwise SNP distances given a multiple sequence alignment.

Usage: pairsnp-rs [OPTIONS] --input <INPUT>

Options:
  -i, --input <INPUT>          Input FASTA file containing multiple sequence alignment
  -o, --output <OUTPUT>        Output file to write pairwise SNP distance matrix (optional, writes to stdout if not specified)
  -t, --nthreads <NTHREADS>    Number of threads to use (optional, default is 1)
  -c, --csv                    Output in CSV format instead of TSV (optional, default output is TSV)
  -s, --sparse                 Sparse output i.e. only non-zero distances and in s1,s2,dist format (optional, default output is dense)
  -d, --threshold <THRESHOLD>  Distance threshold for sparse output (optional, default is no threshold)
  -x, --indices                Output indices instead of sequence IDs (optional, default output is sequence IDs)
  -h, --help                   Print help
  -V, --version                Print version