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.

AuthorMartin Morgan, Michael Lawrence, Simon Anders
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.32.0

View on Bioconductor

Man pages

accessors: (Legacy) Accessors for ShortRead classes

AlignedDataFrame: (Legacy) AlignedDataFrame constructor

AlignedDataFrame-class: (Legacy) "AlignedDataFrame" representing alignment...

AlignedRead: (Legacy) Construct objects of class "AlignedRead"

AlignedRead-class: (Legacy) "AlignedRead" class for aligned short reads

alphabetByCycle: Summarize nucleotide, amino acid, or quality scores by cycle

alphabetScore: Efficiently calculate the sum of quality scores across bases

BowtieQA-class: (Legacy) Quality assessment summaries from Bowtie files

clean: Remove sequences with ambiguous nucleotides from short read...

countLines: Count lines in all (text) files in a directory whose file...

deprecated: Deprecated and defunct functions

dotQA-class: Virtual class for representing quality assessment results

dustyScore: Summarize low-complexity sequences

ExperimentPath-class: (Legacy) "ExperimentPath" class representing a file hierarchy...

FastqQA-class: Quality assessment of fastq files and ShortReadQ objects

filterFastq: Filter fastq from one file to another

Intensity-class: (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure"...

MAQMapQA-class: (Legacy) Quality assessment summaries from MAQ map files

polyn: Utilities for common, simple operations

qa: Perform quality assessment on short reads

qa2: (Updated) quality assessment reports on short reads

QA-class: (Updated) classes for representing quality assessment results

QualityScore: Construct objects indicating read or alignment quality

QualityScore-class: Quality scores for short reads and their alignments

readAligned: (Legacy) Read aligned reads and their quality scores into R...

readBaseQuality: (Legacy) Read short reads and their quality scores into R...

readBfaToc: (Legacy) Get a list of the sequences in a Maq .bfa file

readFasta: Read and write FASTA files to or from ShortRead objects

readFastq: Read and write FASTQ-formatted files

readIntensities: (Legacy) Read Illumina image intensity files

readPrb: (Legacy) Read Solexa prb files as fastq-style quality scores

readQseq: (Legacy) Read Solexa qseq files as fastq-style quality scores

readXStringColumns: Read one or more columns into XStringSet (e.g., DNAStringSet)...

renew: Renew (update) a ShortRead object with new values

report: Summarize quality assessment results into a report

RochePath-class: (Legacy) "RochePath" class representing a Roche (454)...

RocheSet-class: (Legacy) Roche (454) experiment-wide data container

RtaIntensity: (Legacy) Construct objects of class "RtaIntensity"

RtaIntensity-class: (Legacy) Class "RtaIntensity"

Sampler-class: Sampling and streaming records from fastq files

ShortRead-class: "ShortRead" class for short reads

ShortRead-deprecated: Deprecated functions from the ShortRead package

ShortRead-package: FASTQ input and manipulation.

ShortReadQ-class: "ShortReadQ" class for short reads and their quality scores

Snapshot-class: Class '"Snapshot"'

SnapshotFunction-class: Class "SnapshotFunction"

SolexaExportQA-class: (Legacy) Quality assessment summaries from Solexa export and...

SolexaIntensity: (Legacy) Construct objects of class "SolexaIntensity" and...

SolexaIntensity-class: Classes "SolexaIntensity" and "SolexaIntensityInfo"

SolexaPath-class: (Legacy) "SolexaPath" class representing a standard output...

SolexaSet-class: (Legacy) "SolexaSet" coordinating Solexa output locations...

SpTrellis-class: Class "SpTrellis"

spViewPerFeature: Tools to visualize genomic data

srdistance: Edit distances between reads and a small number of short...

srduplicated: Order, sort, and find duplicates in XStringSet objects

srFilter: Functions for user-created and built-in ShortRead filters

SRFilter-class: "SRFilter" for representing functions operating on ShortRead...

SRFilterResult-class: "SRFilterResult" for SRFilter output and statistics

SRSet-class: (Legacy) A base class for Roche experiment-wide data

SRUtil-class: ".SRUtil" and related classes

tables: Summarize XStringSet read frequencies

trimTails: Trim ends of reads based on nucleotides or qualities

Files in this package

ShortRead/.Rinstignore
ShortRead/DESCRIPTION
ShortRead/NAMESPACE
ShortRead/NEWS
ShortRead/R
ShortRead/R/AllClasses-Base.R ShortRead/R/AllClasses-QA.R ShortRead/R/AllGenerics-Base.R ShortRead/R/AllGenerics-QA.R ShortRead/R/AllUtilities.R ShortRead/R/Snapshot.R ShortRead/R/SnapshotFunction-helpers.R ShortRead/R/SnapshotFunction.R ShortRead/R/SpTrellis.R ShortRead/R/filterFastq.R ShortRead/R/methods-.QA.R ShortRead/R/methods-.ShortReadBase.R ShortRead/R/methods-AlignedDataFrame.R ShortRead/R/methods-AlignedRead.R ShortRead/R/methods-BowtieQA.R ShortRead/R/methods-ExperimentPath.R ShortRead/R/methods-FastqFile.R ShortRead/R/methods-FastqFileReader.R ShortRead/R/methods-FastqQA.R ShortRead/R/methods-FastqSampler.R ShortRead/R/methods-FastqStreamer.R ShortRead/R/methods-Intensity.R ShortRead/R/methods-MAQMapQA.R ShortRead/R/methods-Misc.R ShortRead/R/methods-QA.R ShortRead/R/methods-QualityScore.R ShortRead/R/methods-RochePath.R ShortRead/R/methods-RocheSet.R ShortRead/R/methods-RtaIntensity.R ShortRead/R/methods-SRError.R ShortRead/R/methods-SRFilter.R ShortRead/R/methods-SRFilterResult.R ShortRead/R/methods-SRList.R ShortRead/R/methods-SRSet.R ShortRead/R/methods-SRVector.R ShortRead/R/methods-ShortRead.R ShortRead/R/methods-ShortReadFile.R ShortRead/R/methods-ShortReadQ.R ShortRead/R/methods-SolexaExportQA.R ShortRead/R/methods-SolexaIntensity.R ShortRead/R/methods-SolexaPath.R ShortRead/R/methods-SolexaRealignQA.R ShortRead/R/methods-SolexaSet.R ShortRead/R/qa.R ShortRead/R/qa_utilities.R ShortRead/R/readAligned.R ShortRead/R/readBaseQuality.R ShortRead/R/readBfaToc.R ShortRead/R/readIntensities.R ShortRead/R/readPrb.R ShortRead/R/readQseq.R ShortRead/R/readXStringColumns.R ShortRead/R/renew.R ShortRead/R/report.R ShortRead/R/spViewPerFeature.R ShortRead/R/trimEnds.R
ShortRead/build
ShortRead/build/vignette.rds
ShortRead/cleanup
ShortRead/configure
ShortRead/configure.ac
ShortRead/inst
ShortRead/inst/CITATION
ShortRead/inst/doc
ShortRead/inst/doc/Overview.R
ShortRead/inst/doc/Overview.Rnw
ShortRead/inst/doc/Overview.pdf
ShortRead/inst/extdata
ShortRead/inst/extdata/Data
ShortRead/inst/extdata/Data/C1-36Firecrest
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
ShortRead/inst/extdata/E-MTAB-1147
ShortRead/inst/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
ShortRead/inst/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
ShortRead/inst/extdata/bowtie
ShortRead/inst/extdata/bowtie/s_1_aligned_bowtie.txt
ShortRead/inst/extdata/maq
ShortRead/inst/extdata/maq/out.aln.1.txt
ShortRead/inst/extdata/maq/out.aln.2.txt
ShortRead/inst/script
ShortRead/inst/script/qa-test.R
ShortRead/inst/template
ShortRead/inst/template/0000-Header.html
ShortRead/inst/template/1000-Overview.html
ShortRead/inst/template/1100-Overview-SolexaRealign.html
ShortRead/inst/template/2000-RunSummary.html
ShortRead/inst/template/3000-ReadDistribution.html
ShortRead/inst/template/4000-CycleSpecific.html
ShortRead/inst/template/5000-PerTile.html
ShortRead/inst/template/6000-Alignment.html
ShortRead/inst/template/7000-MultipleAlignment.html
ShortRead/inst/template/8000-DepthOfCoverage.html
ShortRead/inst/template/9000-AdapterContamination.html
ShortRead/inst/template/9999-Footer.html
ShortRead/inst/template/QA.css
ShortRead/inst/template/QAAdapterContamination.html
ShortRead/inst/template/QAFiltered.html
ShortRead/inst/template/QAFlagged.html
ShortRead/inst/template/QAFooter.html
ShortRead/inst/template/QAFrequentSequence.html
ShortRead/inst/template/QAHeader.html
ShortRead/inst/template/QANucleotideByCycle.html
ShortRead/inst/template/QANucleotideUse.html
ShortRead/inst/template/QAQualityByCycle.html
ShortRead/inst/template/QAQualityUse.html
ShortRead/inst/template/QAReadQuality.html
ShortRead/inst/template/QASequenceUse.html
ShortRead/inst/template/QASources.html
ShortRead/inst/template/image
ShortRead/inst/template/image/bioclogo-small.gif
ShortRead/inst/template/qa_solexa.Rnw
ShortRead/inst/unitTests
ShortRead/inst/unitTests/cases
ShortRead/inst/unitTests/cases/PE_export.txt.gz
ShortRead/inst/unitTests/cases/s_1_0001_int_head.txt.p
ShortRead/inst/unitTests/cases/s_1_0001_nse_head.txt.p
ShortRead/inst/unitTests/cases/s_1_0001_pos_head.txt
ShortRead/inst/unitTests/cases/s_1_results_head.txt
ShortRead/inst/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
ShortRead/inst/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
ShortRead/inst/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
ShortRead/inst/unitTests/cases/s_1_sequence.9_lines.txt
ShortRead/inst/unitTests/cases/s_1_sequence.txt
ShortRead/inst/unitTests/cases/s_2_0001_realign_3col_head.txt
ShortRead/inst/unitTests/cases/s_2_0001_realign_head.txt
ShortRead/inst/unitTests/cases/s_2_export_run_as_factor.txt
ShortRead/inst/unitTests/cases/s_2_export_toIUPAC.txt
ShortRead/inst/unitTests/cases/sanger.fastq
ShortRead/inst/unitTests/cases/soap.txt
ShortRead/inst/unitTests/cases/solexa.fastq
ShortRead/inst/unitTests/test_AlignedRead.R
ShortRead/inst/unitTests/test_AllClasses.R
ShortRead/inst/unitTests/test_FastqFile.R
ShortRead/inst/unitTests/test_Intensity.R
ShortRead/inst/unitTests/test_SRError.R
ShortRead/inst/unitTests/test_SRFilter.R
ShortRead/inst/unitTests/test_SRFilterResult.R
ShortRead/inst/unitTests/test_SRList.R
ShortRead/inst/unitTests/test_SRVector.R
ShortRead/inst/unitTests/test_ShortRead.R
ShortRead/inst/unitTests/test_ShortReadQ.R
ShortRead/inst/unitTests/test_SolexaIntensity.R
ShortRead/inst/unitTests/test_append.R
ShortRead/inst/unitTests/test_coverage.R
ShortRead/inst/unitTests/test_filterFastq.R
ShortRead/inst/unitTests/test_functions.R
ShortRead/inst/unitTests/test_qa.R
ShortRead/inst/unitTests/test_readPrb.R
ShortRead/inst/unitTests/test_readQseq.R
ShortRead/inst/unitTests/test_readXStringColumns.R
ShortRead/inst/unitTests/test_renew.R
ShortRead/inst/unitTests/test_trimEnds.R
ShortRead/inst/unitTests/test_trimTails.R
ShortRead/inst/unitTests/test_writeFastq.R
ShortRead/man
ShortRead/man/AlignedDataFrame-class.Rd ShortRead/man/AlignedDataFrame.Rd ShortRead/man/AlignedRead-class.Rd ShortRead/man/AlignedRead.Rd ShortRead/man/BowtieQA-class.Rd ShortRead/man/ExperimentPath-class.Rd ShortRead/man/FastqQA-class.Rd ShortRead/man/Intensity-class.Rd ShortRead/man/MAQMapQA-class.Rd ShortRead/man/QA-class.Rd ShortRead/man/QualityScore-class.Rd ShortRead/man/QualityScore.Rd ShortRead/man/RochePath-class.Rd ShortRead/man/RocheSet-class.Rd ShortRead/man/RtaIntensity-class.Rd ShortRead/man/RtaIntensity.Rd ShortRead/man/SRFilter-class.Rd ShortRead/man/SRFilterResult-class.Rd ShortRead/man/SRSet-class.Rd ShortRead/man/SRUtil-class.Rd ShortRead/man/Sampler-class.Rd ShortRead/man/ShortRead-class.Rd ShortRead/man/ShortRead-deprecated.Rd ShortRead/man/ShortRead-package.Rd ShortRead/man/ShortReadQ-class.Rd ShortRead/man/Snapshot-class.Rd ShortRead/man/SnapshotFunction-class.Rd ShortRead/man/SolexaExportQA-class.Rd ShortRead/man/SolexaIntensity-class.Rd ShortRead/man/SolexaIntensity.Rd ShortRead/man/SolexaPath-class.Rd ShortRead/man/SolexaSet-class.Rd ShortRead/man/SpTrellis-class.Rd ShortRead/man/accessors.Rd ShortRead/man/alphabetByCycle.Rd ShortRead/man/alphabetScore.Rd ShortRead/man/clean.Rd ShortRead/man/countLines.Rd ShortRead/man/deprecated.Rd ShortRead/man/dotQA-class.Rd ShortRead/man/dustyScore.Rd ShortRead/man/filterFastq.Rd ShortRead/man/polyn.Rd ShortRead/man/qa.Rd ShortRead/man/qa2.Rd ShortRead/man/readAligned.Rd ShortRead/man/readBaseQuality.Rd ShortRead/man/readBfaToc.Rd ShortRead/man/readFasta.Rd ShortRead/man/readFastq.Rd ShortRead/man/readIntensities.Rd ShortRead/man/readPrb.Rd ShortRead/man/readQseq.Rd ShortRead/man/readXStringColumns.Rd ShortRead/man/renew.Rd ShortRead/man/report.Rd ShortRead/man/spViewPerFeature.Rd ShortRead/man/srFilter.Rd ShortRead/man/srdistance.Rd ShortRead/man/srduplicated.Rd ShortRead/man/tables.Rd ShortRead/man/trimTails.Rd
ShortRead/src
ShortRead/src/Biostrings_stubs.c
ShortRead/src/IRanges_stubs.c
ShortRead/src/Makevars.in
ShortRead/src/Makevars.win
ShortRead/src/R_init_ShortRead.c
ShortRead/src/S4Vectors_stubs.c
ShortRead/src/ShortRead.h
ShortRead/src/XVector_stubs.c
ShortRead/src/alphabet.c
ShortRead/src/call.h
ShortRead/src/const.h
ShortRead/src/io.c
ShortRead/src/io_bowtie.c
ShortRead/src/io_soap.c
ShortRead/src/maqmap_m.h
ShortRead/src/readBfaToc.cc
ShortRead/src/read_maq_map.cc
ShortRead/src/sampler.c
ShortRead/src/trim.c
ShortRead/src/trim.h
ShortRead/src/util.c
ShortRead/src/xsnap.c
ShortRead/tests
ShortRead/tests/ShortRead_unit_tests.R
ShortRead/vignettes
ShortRead/vignettes/Overview.Rnw
ShortRead/vignettes/README
ShortRead/vignettes/ShortRead_and_HilbertVis.Rnw_
ShortRead/vignettes/ShortRead_and_HilbertVis.pdf
ShortRead/vignettes/hilbert.bib
ShortRead/vignettes/images
ShortRead/vignettes/images/HilbertDisplay_GUI.pdf
ShortRead/vignettes/images/HilbertDisplay_GUI.png
ShortRead/vignettes/images/HilbertPlot_H3K4me1.pdf
ShortRead/vignettes/images/HilbertPlot_H3K4me1.png
ShortRead/vignettes/images/HilbertPlot_H3K4me3.pdf
ShortRead/vignettes/images/HilbertPlot_H3K4me3.png
ShortRead/vignettes/images/Strand_and_Dir.pdf
ShortRead/vignettes/images/hilbert_3col.pdf
ShortRead/vignettes/images/hilbert_3col.png
ShortRead/vignettes/qa_E-MTAB-1147.Rda
ShortRead/vignettes/simon2.bst

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