DOI: 10.18129/B9.bioc.ShortRead    

This is the development version of ShortRead; for the stable release version, see ShortRead.

FASTQ input and manipulation

Bioconductor version: Development (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>

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


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

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

# The following initializes usage of Bioc devel


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


PDF   Reference Manual


biocViews DataImport, QualityControl, Sequencing, Software
Version 1.53.0
In Bioconductor since BioC 2.3 (R-2.8) (13 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, dada2, easyRNASeq, FastqCleaner, GOTHiC, icetea, IONiseR, MACPET, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff, systemPipeRdata, UMI4Cats
Suggests Me BiocParallel, CSAR, GenomicAlignments, HiCDataLymphoblast, PING, Repitools, Rsamtools, S4Vectors, yeastRNASeq
Links To Me
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