R Observatory: Metrics for Rbowtie2 version 2.18.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rbowtie2

Bioc current

An R Wrapper for Bowtie2 and AdapterRemoval

v2.18.0 · software · GPL (>= 3)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.6 · Oct 31, 2017

Current · Requires R 4.6

1.0 In 18 of 49 releases 3.23

Description

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

8347 10 exported

Complexity

5.4 avg / 29 max

Call network

8347 nodes / 11151 edges

Test coverage is not measured for Bioconductor packages; 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.

Code

Structure

Lines of code

286,952

Files

574

Compiled share

99.3%

Has compiled src

Yes

Language breakdown

R 969 (0.3%)C/C++/src 285,025 (99.3%)Docs 745 (0.3%)Vignettes 213 (0.1%)

API

Exported functions

10

Internal functions

7

Recent export changes

v3.6+9 adapterremoval_usage, adapterremoval_version, bowtie2 +6 more

Testing & CI

Has tests

No

Test-to-code ratio

0.00

testthat edition

3

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1.0

System requirements

3

C++ standard

–

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

18

First release

2018-02-22

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

2

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 334 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 63%

Topics

Software › Technology › Sequencing

Software › WorkflowStep › Alignment

Software › WorkflowStep › Preprocessing

Depended on by (4)

Bioconductor (4)

CircSeqAlignTk esATAC UMI4Cats MetaScope

People

Zheng Wei author maintainer
Wei Zhang author

At a glance

Version: 2.18.0
Category: software
License: GPL (>= 3)
Requires R: ≥ 4.6
Maintainer: Zheng Wei
Entered: 3.6 · Oct 31, 2017
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.1.0)

Imports

magrittrRsamtoolsBioc

Suggests

knitr testthat (>= 3.0.0)rmarkdown

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Rbowtie2")

Format

Wei, Z., & Zhang, W. (2026). Rbowtie2: An R Wrapper for Bowtie2 and AdapterRemoval (Version 2.18.0) [Computer software]. https://bioconductor.org/packages/Rbowtie2

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for Rbowtie2 version 2.18.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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