Package: ShortRead 1.71.1

Bioconductor Package Maintainer

ShortRead: FASTQ input and manipulation

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.

Authors:Bioconductor Package Maintainer [cre], Martin Morgan [aut], Michael Lawrence [ctb], Simon Anders [ctb], Rohit Satyam [ctb], J Wokaty [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ShortRead/json (API)

# Install 'ShortRead' in R:

install.packages('ShortRead', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/shortread/issues

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:ShortRead-1.71.0(bioc 3.24)ShortRead-1.70.0(bioc 3.23)

dataimport sequencing qualitycontrol bioconductor-package core-package zlib cpp

11.38 score 8 stars 54 packages 2.2k scripts 119 mentions 175 exports 44 dependencies

Last updated from:6d09fd11bd. Checks:1 WARNING, 11 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	213
linux-devel-arm64	ERROR	318
linux-devel-x86_64	ERROR	408
source / vignettes	OK	315
linux-release-arm64	ERROR	301
linux-release-x86_64	ERROR	385
macos-release-arm64	ERROR	186
macos-release-x86_64	ERROR	474
macos-oldrel-arm64	ERROR	183
macos-oldrel-x86_64	ERROR	563
windows-devel	ERROR	385
windows-release	ERROR	395
windows-oldrel	ERROR	399
wasm-release	OK	192

Exports:%in%alignData alignDataFilter AlignedDataFrame AlignedRead alignQuality alignQualityFilter alphabet alphabetByCycle alphabetFrequency alphabetScore analysisPath annTrack append ArrayIntensity baseCallPath basePath chromosome chromosomeFilter clean close.ShortReadFile coerce compose countFastq countLines coverage dataPath dustyFilter dustyScore encoding experimentPath ExperimentPath fac FastqFile FastqFileList FastqQuality FastqSampler FastqSamplerList FastqStreamer FastqStreamerList files filterFastq flag functions getTrellis id idFilter ignore.strand imageAnalysisPath IntegerQuality intensity laneDescription laneNames lapply left limits MatrixQuality measurementError name narrow nFilter NumericQuality occurrenceFilter open.ShortReadFile pan pData phenoData polyn polynFilter position positionFilter qa QA qa2 QAAdapterContamination QACollate QAData QAFastqSource QAFiltered QAFlagged QAFrequentSequence QANucleotideByCycle QANucleotideUse QAQualityByCycle QAQualityUse QAReadQuality QASequenceUse qualPath rbind read454 readAligned readBaseQuality readBfaToc readCount readData reader readFasta readFastaQual readFastq readIndex readIntensities readIntensityInfo readPath readPrb readQseq readQual readXStringColumns renew renewable report report_html restore reverse reverseComplement right RochePath RocheSet RtaIntensity runNames sapply scanPath SFastqQuality ShortRead ShortReadQ show Snapshot SnapshotFunction SnapshotFunctionList SolexaIntensity SolexaIntensityInfo solexaPath SolexaPath SolexaSet sourcePath SpTrellis spViewPerFeature srdistance srdistanceFilter srduplicated sread SRError srFilter SRFilterResult srlist SRList srorder srrank srsort SRVector SRWarn stats strand strandFilter tables togglefun togglep togglez trimEnds trimLRPatterns trimTails trimTailw uniqueFilter varLabels varMetadata vclass view viewer vrange width writeFasta writeFastq yield zi zo zoom

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon DelayedArray deldir formatR futile.logger futile.options generics GenomicAlignments GenomicRanges hwriter interp IRanges jpeg lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats png pwalign RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment XVector

An Introduction to ShortRead

Rendered fromOverview.Rmdusingknitr::rmarkdown

Last update: 2024-04-23
Started: 2024-01-03

Help page	Topics
FASTQ input and manipulation.	ShortRead-package .Roche-class .ShortReadBase-class .Solexa-class append,.ShortReadBase,.ShortReadBase-method show,.ShortReadBase-method
Virtual class for representing quality assessment results	.QA-class rbind,.QA-method show,.QA-method
(Legacy) Accessors for ShortRead classes	accessors alignData alignQuality analysisPath baseCallPath chromosome dataPath experimentPath imageAnalysisPath laneDescription laneNames position scanPath solexaPath vclass
(Legacy) AlignedDataFrame constructor	AlignedDataFrame
(Legacy) "AlignedDataFrame" representing alignment annotations as a data frame	AlignedDataFrame-class append,AlignedDataFrame,AlignedDataFrame-method
(Legacy) Construct objects of class "AlignedRead"	AlignedRead
(Legacy) "AlignedRead" class for aligned short reads	%in%,AlignedRead,IntegerRangesList-method AlignedRead-class append,AlignedRead,AlignedRead-method chromosome,AlignedRead-method coerce,AlignedRead,GAlignments-method coerce,AlignedRead,GappedReads-method coerce,AlignedRead,GRanges-method coerce,AlignedRead,IntegerRangesList-method coerce,PairwiseAlignments,AlignedRead-method coverage,AlignedRead-method detail,AlignedRead-method position,AlignedRead-method show,AlignedRead-method srduplicated,AlignedRead-method srorder,AlignedRead-method srrank,AlignedRead-method strand,AlignedRead-method [,AlignedRead,ANY,ANY,ANY-method [,AlignedRead,ANY,ANY-method [,AlignedRead,ANY,missing,ANY-method [,AlignedRead,ANY,missing-method [,AlignedRead,missing,ANY,ANY-method [,AlignedRead,missing,ANY-method [,AlignedRead,missing,missing,ANY-method [,AlignedRead,missing,missing-method
Summarize nucleotide, amino acid, or quality scores by cycle	alphabetByCycle alphabetByCycle,BStringSet-method
Efficiently calculate the sum of quality scores across bases	alphabetScore
(Legacy) Quality assessment summaries from Bowtie files	BowtieQA-class report,BowtieQA-method report_html,BowtieQA-method
Remove sequences with ambiguous nucleotides from short read classes	clean clean,DNAStringSet-method
Count lines in all (text) files in a directory whose file name matches a pattern	countLines
Deprecated and defunct functions	basePath defunct deprecated readAligned,BamFile-method srapply
Summarize low-complexity sequences	dustyScore dustyScore,DNAStringSet-method dustyScore,ShortRead-method
(Legacy) "ExperimentPath" class representing a file hierarchy of data files	detail,ExperimentPath-method ExperimentPath ExperimentPath-class show,ExperimentPath-method
Sampling and streaming records from fastq files	close.ShortReadFile countFastq,FastqFile-method FastqFile FastqFile-class FastqFileList FastqFileList,ANY-method FastqFileList,character-method FastqFileList-class FastqFileReader-class FastqSampler FastqSampler-class FastqSamplerList FastqSamplerList,ANY-method FastqSamplerList,character-method FastqSamplerList-class FastqStreamer FastqStreamer,ANY,IRanges-method FastqStreamer,ANY,missing-method FastqStreamer,ANY,numeric-method FastqStreamer-class FastqStreamerList FastqStreamerList,ANY-method FastqStreamerList,character-method FastqStreamerList-class open.ShortReadFile readFastq,FastqFile-method ShortReadFile-class yield yield,FastqFileReader-method yield,FastqSampler-method yield,FastqStreamer-method
Filter fastq from one file to another	filterFastq
(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities	ArrayIntensity ArrayIntensity-class dim,Intensity-method intensity Intensity-class IntensityInfo-class IntensityMeasure-class measurementError readIntensityInfo show,Intensity-method show,IntensityMeasure-method [,IntensityMeasure,ANY,ANY,ANY-method [,IntensityMeasure,ANY,ANY-method [,IntensityMeasure,ANY,missing,ANY-method [,IntensityMeasure,missing,ANY,ANY-method [,IntensityMeasure,missing,missing,ANY-method [[,ArrayIntensity,ANY,ANY-method
(Legacy) Quality assessment summaries from MAQ map files	MAQMapQA MAQMapQA-class report,MAQMapQA-method report_html,MAQMapQA-method
Perform quality assessment on short reads	qa qa,character-method qa,list-method
(Updated) classes for representing quality assessment results	.QA2-class QA-class QAAdapterContamination-class QACollate-class QAData-class QAFastqSource-class QAFiltered-class QAFlagged-class QAFrequentSequence-class QANucleotideByCycle-class QANucleotideUse-class QAQualityByCycle-class QAQualityUse-class QAReadQuality-class QASequenceUse-class QASource-class QASummary-class
(Updated) quality assessment reports on short reads	flag flag,.QA2-method flag,QAFrequentSequence-method flag,QAReadQuality-method flag,QASource-method QA qa2 qa2,FastqSampler-method qa2,QAAdapterContamination-method qa2,QACollate-method qa2,QAFastqSource-method qa2,QAFrequentSequence-method qa2,QANucleotideByCycle-method qa2,QANucleotideUse-method qa2,QAQualityByCycle-method qa2,QAQualityUse-method qa2,QAReadQuality-method qa2,QASequenceUse-method QAAdapterContamination QACollate QACollate,missing-method QACollate,QAFastqSource-method QAData QAFastqSource QAFiltered QAFlagged QAFrequentSequence QANucleotideByCycle QANucleotideUse QAQualityByCycle QAQualityUse QAReadQuality QASequenceUse rbind,QASummary-method report,QA-method report,QAAdapterContamination-method report,QAFiltered-method report,QAFlagged-method report,QAFrequentSequence-method report,QANucleotideByCycle-method report,QANucleotideUse-method report,QAQualityByCycle-method report,QAQualityUse-method report,QAReadQuality-method report,QASequenceUse-method report,QASource-method show,QAAdapterContamination-method show,QACollate-method show,QAFastqSource-method show,QAFrequentSequence-method show,QAReadQuality-method show,QASummary-method
Construct objects indicating read or alignment quality	FastqQuality FastqQuality,BStringSet-method FastqQuality,character-method FastqQuality,missing-method IntegerQuality MatrixQuality NumericQuality SFastqQuality SFastqQuality,BStringSet-method SFastqQuality,character-method SFastqQuality,missing-method
Quality scores for short reads and their alignments	alphabet,FastqQuality-method alphabetByCycle,FastqQuality-method alphabetFrequency,FastqQuality-method alphabetScore,FastqQuality-method alphabetScore,PhredQuality-method alphabetScore,SFastqQuality-method append,MatrixQuality,MatrixQuality-method append,QualityScore,QualityScore-method coerce,FastqQuality,matrix-method coerce,FastqQuality,numeric-method coerce,FastqQuality,PhredQuality-method coerce,SFastqQuality,matrix-method coerce,SFastqQuality,SolexaQuality-method detail,QualityScore-method dim,MatrixQuality-method encoding,FastqQuality-method encoding,SFastqQuality-method FastqQuality-class IntegerQuality-class length,MatrixQuality-method length,QualityScore-method MatrixQuality-class narrow,FastqQuality-method narrow,MatrixQuality-method NumericQuality-class QualityScore-class reverse,FastqQuality-method SFastqQuality-class show,FastqQuality-method show,NumericQuality-method srduplicated,FastqQuality-method srorder,FastqQuality-method srrank,FastqQuality-method srsort,FastqQuality-method trimTails,FastqQuality-method trimTailw,FastqQuality-method width,FastqQuality-method width,MatrixQuality-method width,NumericQuality-method width,QualityScore-method [,MatrixQuality,ANY,missing,ANY-method [,MatrixQuality,ANY,missing-method [,QualityScore,ANY,missing,ANY-method [,QualityScore,ANY,missing-method [[,MatrixQuality,ANY,missing-method [[,QualityScore,ANY,missing-method
(Legacy) Read aligned reads and their quality scores into R representations	readAligned readAligned,character-method
(Legacy) Read short reads and their quality scores into R representations	readBaseQuality readBaseQuality,character-method
(Legacy) Get a list of the sequences in a Maq .bfa file	readBfaToc
Read and write FASTA files to or from ShortRead objects	readFasta readFasta,character-method writeFasta writeFasta,DNAStringSet-method
Read, write, and count records in FASTQ-formatted files	countFastq countFastq,character-method readFastq readFastq,character-method writeFastq
(Legacy) Read Illumina image intensity files	readIntensities readIntensities,character-method
(Legacy) Read Solexa prb files as fastq-style quality scores	readPrb readPrb,character-method
(Legacy) Read Solexa qseq files as fastq-style quality scores	readQseq readQseq,character-method
Read one or more columns into XStringSet (e.g., DNAStringSet) objects	readXStringColumns
Renew (update) a ShortRead object with new values	renew renew,.ShortReadBase-method renewable renewable,.ShortReadBase-method renewable,character-method renewable,missing-method
Summarize quality assessment results into a report	report report,ANY-method report_html
(Legacy) "RochePath" class representing a Roche (454) experiment location	detail,RochePath-method qualPath read454 read454,RochePath-method readBaseQuality,RochePath-method readFasta,RochePath-method readFastaQual readFastaQual,character-method readFastaQual,RochePath-method readPath readQual readQual,character-method readQual,RochePath-method RochePath RochePath-class RocheSet,character-method RocheSet,RochePath-method runNames runNames,RochePath-method show,RochePath-method
(Legacy) Roche (454) experiment-wide data container	RocheSet RocheSet-class
(Legacy) Construct objects of class "RtaIntensity"	RtaIntensity
(Legacy) Class "RtaIntensity"	RtaIntensity-class
"ShortRead" class for short reads	alphabetByCycle,ShortRead-method append,ShortRead,ShortRead-method clean,ShortRead-method coerce,ShortRead,DNAStringSet-method detail,ShortRead-method id id,ShortRead-method length,ShortRead-method narrow,ShortRead-method ShortRead ShortRead,DNAStringSet,BStringSet-method ShortRead,DNAStringSet,missing-method ShortRead,missing,missing-method ShortRead-class show,ShortRead-method srdistance,ShortRead,ANY-method srduplicated,ShortRead-method sread sread,ShortRead-method srorder,ShortRead-method srrank,ShortRead-method srsort,ShortRead-method tables,ShortRead-method trimLRPatterns,ShortRead-method width,ShortRead-method writeFasta,ShortRead-method [,ShortRead,ANY,ANY,ANY-method [,ShortRead,ANY,ANY-method [,ShortRead,ANY,missing,ANY-method [,ShortRead,ANY,missing-method [,ShortRead,missing,ANY,ANY-method [,ShortRead,missing,ANY-method [,ShortRead,missing,missing,ANY-method [,ShortRead,missing,missing-method
Deprecated functions from the ShortRead package	uniqueFilter
"ShortReadQ" class for short reads and their quality scores	alphabetByCycle,ShortReadQ-method alphabetScore,ShortReadQ-method append,ShortReadQ,ShortReadQ-method coerce,ShortReadQ,QualityScaledDNAStringSet-method detail,ShortReadQ-method narrow,ShortReadQ-method qa,ShortReadQ-method reverse,ShortReadQ-method reverseComplement,ShortReadQ-method ShortReadQ ShortReadQ,DNAStringSet,BStringSet,BStringSet-method ShortReadQ,DNAStringSet,BStringSet,missing-method ShortReadQ,DNAStringSet,QualityScore,BStringSet-method ShortReadQ,DNAStringSet,QualityScore,missing-method ShortReadQ,missing,missing,missing-method ShortReadQ-class trimTails,ShortReadQ-method trimTailw,ShortReadQ-method writeFastq,ShortReadQ,character-method writeFastq,ShortReadQ,FastqFile-method [,ShortReadQ,ANY,ANY,ANY-method [,ShortReadQ,ANY,ANY-method [,ShortReadQ,ANY,missing,ANY-method [,ShortReadQ,ANY,missing-method [,ShortReadQ,missing,ANY,ANY-method [,ShortReadQ,missing,ANY-method [,ShortReadQ,missing,missing,ANY-method [,ShortReadQ,missing,missing-method [<-,ShortReadQ,ANY,missing,ShortReadQ-method
Quality assessment of fastq files and ShortReadQ objects	FastqQA FastqQA-class report,FastqQA-method report_html,FastqQA-method report_html,ShortReadQQA-method ShortReadQQA-class
Class '"Snapshot"'	annTrack annTrack,Snapshot-method fac fac,Snapshot-method files files,Snapshot-method functions functions,Snapshot-method getTrellis getTrellis,Snapshot-method ignore.strand ignore.strand,Snapshot-method pan pan,Snapshot-method show,Snapshot-method Snapshot Snapshot,BamFileList,GRanges-method Snapshot,character,GRanges-method Snapshot,character,missing-method Snapshot-class togglefun togglefun,Snapshot-method togglep togglep,Snapshot-method togglez togglez,Snapshot-method trellis-class view view,Snapshot-method vrange vrange,Snapshot-method zoom zoom,Snapshot-method
Class "SnapshotFunction"	limits reader show,SnapshotFunction-method SnapshotFunction SnapshotFunction-class SnapshotFunctionList SnapshotFunctionList,ANY-method SnapshotFunctionList,SnapshotFunction-method SnapshotFunctionList-class viewer
(Legacy) Quality assessment summaries from Solexa export and realign files	report,SolexaExportQA-method report_html,SolexaExportQA-method report_html,SolexaRealignQA-method show,SolexaExportQA-method SolexaExportQA SolexaExportQA-class SolexaRealignQA-class
(Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"	SolexaIntensity SolexaIntensityInfo
Classes "SolexaIntensity" and "SolexaIntensityInfo"	SolexaIntensity-class SolexaIntensityInfo-class [,SolexaIntensity,ANY,ANY,ANY-method [,SolexaIntensity,ANY,ANY-method [,SolexaIntensity,ANY,missing,ANY-method [,SolexaIntensity,missing,ANY,ANY-method [,SolexaIntensity,missing,missing,ANY-method
(Legacy) "SolexaPath" class representing a standard output file hierarchy	detail,SolexaPath-method qa,SolexaPath-method readAligned,SolexaPath-method readBaseQuality,SolexaPath-method readFasta,SolexaPath-method readFastq,SolexaPath-method readIntensities,SolexaPath-method readPrb,SolexaPath-method readQseq,SolexaPath-method report,SolexaPath-method show,SolexaPath-method SolexaPath SolexaPath-class SolexaSet,SolexaPath-method
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations	detail,SolexaSet-method laneNames,AnnotatedDataFrame-method laneNames,SolexaSet-method readAligned,SolexaSet-method show,SolexaSet-method SolexaSet SolexaSet,character-method SolexaSet-class
Class "SpTrellis"	left left,SpTrellis-method restore restore,SpTrellis-method right right,SpTrellis-method show,SpTrellis-method SpTrellis SpTrellis-class zi zi,SpTrellis-method zo zo,SpTrellis-method
Tools to visualize genomic data	spViewPerFeature
Edit distances between reads and a small number of short references	srdistance srdistance,DNAStringSet,character-method srdistance,DNAStringSet,DNAString-method srdistance,DNAStringSet,DNAStringSet-method
Order, sort, and find duplicates in XStringSet objects	srduplicated srduplicated,XStringSet-method srorder srorder,XStringSet-method srrank srrank,XStringSet-method srsort srsort,XStringSet-method
Functions for user-created and built-in ShortRead filters	alignDataFilter alignQualityFilter chromosomeFilter compose dustyFilter idFilter nFilter occurrenceFilter polynFilter positionFilter srdistanceFilter srFilter srFilter,function-method srFilter,missing-method strandFilter
"SRFilter" for representing functions operating on ShortRead objects	c,SRFilter-method coerce,SRFilter,FilterRules-method name name,SRFilter-method show,SRFilter-method srFilter,SRFilter-method SRFilter-class
"SRFilterResult" for SRFilter output and statistics	!,SRFilterResult-method Logic,SRFilterResult,SRFilterResult-method name,SRFilterResult-method show,SRFilterResult-method SRFilterResult SRFilterResult-class stats stats,SRFilterResult-method
(Legacy) A base class for Roche experiment-wide data	detail,SRSet-method experimentPath,SRSet-method phenoData,SRSet-method readCount readData readIndex show,SRSet-method sourcePath SRSet-class
".SRUtil" and related classes	.SRUtil-class detail,.ShortReadBase-method detail,SRList-method detail,SRVector-method lapply,SRList,ANY-method lapply,SRList-method length,SRList-method names,SRList-method names<-,SRList,character-method sapply,SRList-method show,SRList-method show,SRVector-method SRError SRError-class SRList srlist SRList-class SRVector SRVector-class SRWarn SRWarn-class [,SRList,ANY,missing,ANY-method [,SRList,ANY,missing-method [[,SRList,ANY,missing-method
Summarize XStringSet read frequencies	tables tables,XStringSet-method
Trim ends of reads based on nucleotides or qualities	trimEnds trimEnds,character-method trimEnds,FastqQuality-method trimEnds,ShortRead-method trimEnds,ShortReadQ-method trimEnds,XStringQuality-method trimEnds,XStringSet-method trimTails trimTails,BStringSet-method trimTails,character-method trimTails,XStringQuality-method trimTailw trimTailw,BStringSet-method trimTailw,character-method trimTailw,XStringQuality-method
Utilities for common, simple operations	polyn

Package: ShortRead 1.71.1

ShortRead: FASTQ input and manipulation

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