DOI: 10.18129/B9.bioc.ShortRead  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ShortRead.

FASTQ input and manipulation

Bioconductor version: 3.16

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: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Michael Lawrence [ctb], Simon Anders [ctb]

Maintainer: Bioconductor Package Maintainer <maintainer at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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PDF R Script An introduction to ShortRead
PDF   Reference Manual
Text   NEWS


biocViews DataImport, QualityControl, Sequencing, Software
Version 1.56.1
In Bioconductor since BioC 2.3 (R-2.8) (14.5 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
LinkingTo S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
Depends On Me chipseq, EatonEtAlChIPseq, EDASeq, esATAC, girafe, HTSeqGenie, NestLink, OTUbase, Rqc, segmentSeq, sequencing, systemPipeR
Imports Me amplican, ArrayExpressHTS, basecallQC, BEAT, CellBarcode, chipseq, ChIPseqR, ChIPsim, CircSeqAlignTk, dada2, easyRNASeq, FastqCleaner, GOTHiC, icetea, IONiseR, MACPET, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff, UMI4Cats
Suggests Me BiocParallel, CSAR, FLAMES, GenomicAlignments, HiCDataLymphoblast, PING, Repitools, Rsamtools, S4Vectors, systemPipeRdata, yeastRNASeq
Links To Me
Build Report  

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Source Package ShortRead_1.56.1.tar.gz
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