ShortRead

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ShortRead.

FASTQ input and manipulation

Bioconductor version: 3.15

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.

Author: Martin Morgan, Michael Lawrence, Simon Anders

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("ShortRead")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("ShortRead")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ShortRead")

An introduction to ShortRead PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, QualityControl, Sequencing, Software

Version 1.54.0

In Bioconductor since BioC 2.3 (R-2.8) (15.5 years)

License Artistic-2.0

Depends BiocGenerics(>= 0.23.3), BiocParallel, Biostrings(>= 2.47.6), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6)

Imports Biobase, S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra

System Requirements

URL

Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi

Linking To S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc

Enhances