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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "ssw" in publications use:'
type: software
license: MIT
title: 'ssw: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD'
version: 0.2.1
doi: 10.1371/journal.pone.0082138
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ssw
abstract: Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python'
  binding 'ssw-py'. 'SSW' is a fast 'C' and 'C++' implementation of the Smith-Waterman
  algorithm for pairwise sequence alignment using Single-Instruction-Multiple-Data
  (SIMD) instructions. 'SSW' enhances the standard algorithm by efficiently returning
  alignment information and suboptimal alignment scores. The core 'SSW' library offers
  performance improvements for various bioinformatics tasks, including protein database
  searches, short-read alignments, primary and split-read mapping, structural variant
  detection, and read-overlap graph generation. These features make 'SSW' particularly
  useful for genomic applications. Zhao et al. (2013) <https://doi.org/10.1371/journal.pone.0082138>
  developed the original 'C' and 'C++' implementation.
authors:
- family-names: Xiao
  given-names: Nan
  email: me@nanx.me
  orcid: https://orcid.org/0000-0002-0250-5673
preferred-citation:
  type: article
  title: 'SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications'
  authors:
  - family-names: Zhao
    given-names: Mengyao
  - family-names: Lee
    given-names: Wan-Ping
  - family-names: Garrison
    given-names: Erik P
  - family-names: Marth
    given-names: Gabor T
  journal: PloS ONE
  volume: '8'
  issue: '12'
  year: '2013'
  doi: 10.1371/journal.pone.0082138
  start: e82138
repository: https://nanxstats.r-universe.dev
repository-code: https://github.com/nanxstats/ssw-r
commit: 9b36eb0fcb17d5027d3aaf33d2f680200414eeb7
url: https://nanx.me/ssw-r/
contact:
- family-names: Xiao
  given-names: Nan
  email: me@nanx.me
  orcid: https://orcid.org/0000-0002-0250-5673