pairsnp-rs

A Rust implementation for calculating pairwise SNP distance matrices using a multiple sequence alignment. This is heavily inspired by https://github.com/gtonkinhill/pairsnp-cpp and is a project for me to learn Rust.

Installation

cargo install pairsnp-rs

Input

The input file should be a multiple sequence alignment in FASTA format. The tool will handle both regular and gzipped files.

Output

The output will be a matrix of pairwise SNP distances. By default, this will be output to stdout, but can be piped to a file if the user desires or specified using the -o flag.

Usage

The tool can be run from the command line as:

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

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)
  -b, --chunk-size <CHUNK_SIZE>  Chunk size for parallel processing (optional, default is 1024)
  -h, --help                     Print help
  -V, --version                  Print version