Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD • ssw

ssw-r offers an R interface for SSW, a fast implementation of the Smith-Waterman algorithm for sequence alignment using SIMD. ssw-r is currently built on the Python package ssw-py.

Installation

Install ssw-r from GitHub:

remotes::install_github("nanxstats/ssw-r")

Installed ssw-py via pip:

pip3 install ssw-py

Usage

reticulate::use_python("/usr/local/bin/python3")
library("ssw")

"ACGT" %>% align("TTTTACGTCCCCC")
"ACGT" %>% align("TTTTACTCCCCC", gap_open = 3)
"ACTG" %>% force_align("TTTTCTGCCCCCACG") %>% formatter(print = TRUE)

Developers

If you have already installed Python and ssw-py, and want to develop ssw-r in RStudio, simply create a file .Rprofile under the package directory and set the Python binary path (Homebrew Python 3 path example below):

Sys.setenv(RETICULATE_PYTHON = "/usr/local/bin/python3")

The next time you open the project, the correct Python path and library path should be already set. For more technical details, see reticulate Python version configuration.

License

This project is licensed under the MIT license.