ShortRead
Bioc currentFASTQ input and manipulation
Release Lineage
Entered 2.2 · May 1, 2008
Current · Requires R 4.6
Description
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
355 0 exported
Complexity
2.2 avg / 10 max
Call network
355 nodes / 436 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
22,135
Files
251
Compiled share
16.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
34
Internal functions
107
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
0%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
9.7%
Unsafe pattern score
0
Dep constraint coverage
46.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
37
First release
2008-04-30
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
18
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- References docs
- 2%
Topics
Depended on by (62)
Bioconductor (55)
CRAN (7)
People
- Bioconductor Package Maintainer maintainer
- Simon Anders contributor
- Michael Lawrence contributor
- Martin Morgan author
- Rohit Satyam contributor
- J Wokaty contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ShortRead")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.
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.