ShortRead: FASTQ input and manipulation

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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
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.32.0

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