pairsnp-c++

This c++ version makes use of fast bitset operations to speed up distance calculations.

Installation

The c++ version can be installed manually or with conda as

conda install -c bioconda pairsnp

The c++ code can be built by running

cd ./pairsnp-cpp/
make
make install

If your compiler does not have support for open-mp you can run

make ompoff=1

Quick Start

The c++ version can be run from the command line as

pairsnp -c msa.fasta > output.csv

additional options include

SYNOPSIS
  Fast pairwise SNP distance matrices
USAGE
  pairsnp [options] alignment.fasta[.gz] > matrix.csv
OPTIONS
  -h	Show this help
  -v	Print version and exit
  -s	Output in sparse matrix form (i,j,distance).
  -d	Distance threshold for sparse output. Only distances <= d will be returned.
  -k	Will on return the k nearest neighbours for each sample in sparse output.
  -c	Output CSV instead of TSV
  -i	Output sequence index inplace of header (useful for downstream processing)
  -t	Number of threads to use (default=1)