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FASTQ input and manipulation

Bioconductor version: Release (3.19)

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], Rohit Satyam [ctb] (Converted Overview.Rnw vignette from Sweave to RMarkdown / HTML.), J Wokaty [ctb]

Maintainer: Bioconductor Package Maintainer <maintainer at>

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


To install this package, start R (version "4.4") and enter:

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


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


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

An introduction to ShortRead HTML R Script
Reference Manual PDF


biocViews DataImport, QualityControl, Sequencing, Software
Version 1.62.0
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), pwalign, hwriter, methods, zlibbioc, lattice, latticeExtra
System Requirements
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Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr
Linking To S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
Depends On Me chipseq, EDASeq, esATAC, girafe, HTSeqGenie, OTUbase, Rqc, segmentSeq, systemPipeR, EatonEtAlChIPseq, NestLink, sequencing, STRMPS
Imports Me amplican, basecallQC, BEAT, CellBarcode, chipseq, ChIPseqR, ChIPsim, CircSeqAlignTk, dada2, easyRNASeq, FastqCleaner, GOTHiC, icetea, IONiseR, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff, UMI4Cats, seqpac, DBTC, genBaRcode
Suggests Me BiocParallel, CSAR, FLAMES, GenomicAlignments, PING, Repitools, Rsamtools, S4Vectors, HiCDataLymphoblast, systemPipeRdata, yeastRNASeq
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package ShortRead_1.62.0.tar.gz
Windows Binary
macOS Binary (x86_64) ShortRead_1.62.0.tgz
macOS Binary (arm64) ShortRead_1.62.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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