ssw

0.2.1

Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD

0packages depend

6.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Nan XiaoFirst published 2024-09-052 releasesCRAN page ↗GitHub ↗

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) doi:10.1371/journal.pone.0082138 developed the original 'C' and 'C++' implementation.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("ssw", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("nanxstats/ssw-r")

Development version from nanxstats/ssw-r. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ssw

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ssw

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ssw

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.2 min · r-devel-linux-x86_64-fedora-gcc

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-08
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

6.3K

CRAN downloads in the past year

Rank #6,947 · ~17/day · ~529/mo

Releases R versions

Daily download trend is not available in this view yet.

52130 days

1.6K90 days

6.3K1 year

Compare downloads with other packages →

Also on86 r2u14 autocran

Repository

GitHub ↗ nanxstats/ssw-r

6Stars

0Forks

0Open issues

0Open PRs

2Releases

smith-watermansequence-alignmentsimdbioinformaticsreticulate

Stars over time

2025-03-07 · 62026-07-07 · 6

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (1)

reticulate

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

Rd 251 (28%)Vignettes 247 (27%)CSS 212 (23%)R 189 (21%)Other 10 (1%)

Code characteristics

Object systems

S31

Cyclomatic complexity: 1.0 median / 3 max
Documented parameters: 100%
System requirements: 2 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

7 5 exported

Complexity

1.4 avg / 3 max

Call network

7 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Nan Xiao

Author, Maintainer, Copyright holder

Authors (1)

Nan Xiao

Author, Maintainer, Copyright holder

Nan Xiao

Author, Maintainer, Copyright holder

Release timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.2.1Latest
2024-09-18 · current release · diff ↗
0.2.0
2024-09-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-05
Total releases: 2 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 257 KB
Installed size: not tracked yet
With dependencies: not tracked yet