Package: ShortRead 1.65.0
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:
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ShortRead.pdf |ShortRead.html✨
ShortRead/json (API)
NEWS
| # 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
On BioConductor:ShortRead-1.65.0(bioc 3.21)ShortRead-1.64.0(bioc 3.20)
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
Last updated 2 months agofrom:ad4e1dfeb6. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 30 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 30 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 30 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 30 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 30 2024 |
Exports:%in%alignDataalignDataFilterAlignedDataFrameAlignedReadalignQualityalignQualityFilteralphabetalphabetByCyclealphabetFrequencyalphabetScoreanalysisPathannTrackappendArrayIntensitybaseCallPathbasePathchromosomechromosomeFiltercleanclose.ShortReadFilecoercecomposecountFastqcountLinescoveragedataPathdustyFilterdustyScoreencodingexperimentPathExperimentPathfacFastqFileFastqFileListFastqQualityFastqSamplerFastqSamplerListFastqStreamerFastqStreamerListfilesfilterFastqflagfunctionsgetTrellisididFilterignore.strandimageAnalysisPathIntegerQualityintensitylaneDescriptionlaneNameslapplyleftlimitsMatrixQualitymeasurementErrornamenarrownFilterNumericQualityoccurrenceFilteropen.ShortReadFilepanpDataphenoDatapolynpolynFilterpositionpositionFilterqaQAqa2QAAdapterContaminationQACollateQADataQAFastqSourceQAFilteredQAFlaggedQAFrequentSequenceQANucleotideByCycleQANucleotideUseQAQualityByCycleQAQualityUseQAReadQualityQASequenceUsequalPathrbindread454readAlignedreadBaseQualityreadBfaTocreadCountreadDatareaderreadFastareadFastaQualreadFastqreadIndexreadIntensitiesreadIntensityInforeadPathreadPrbreadQseqreadQualreadXStringColumnsrenewrenewablereportreport_htmlrestorereversereverseComplementrightRochePathRocheSetRtaIntensityrunNamessapplyscanPathSFastqQualityShortReadShortReadQshowSnapshotSnapshotFunctionSnapshotFunctionListSolexaIntensitySolexaIntensityInfosolexaPathSolexaPathSolexaSetsourcePathSpTrellisspViewPerFeaturesrdistancesrdistanceFiltersrduplicatedsreadSRErrorsrFilterSRFilterResultsrlistSRListsrordersrranksrsortSRVectorSRWarnstatsstrandstrandFiltertablestogglefuntoggleptoggleztrimEndstrimLRPatternstrimTailstrimTailwuniqueFiltervarLabelsvarMetadatavclassviewviewervrangewidthwriteFastawriteFastqyieldzizozoom
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| FASTQ input and manipulation. | ShortReadBase-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 |
