# FASTQ input and manipulation

## Documentation for package ‘ShortRead’ version 1.60.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N O P Q R S T U V W Y Z misc

ShortReadBase-package | FASTQ input and manipulation.

## -- A --

accessors | (Legacy) Accessors for ShortRead classes
alignData | (Legacy) Accessors for ShortRead classes
alignDataFilter | Functions for user-created and built-in ShortRead filters
AlignedDataFrame | (Legacy) AlignedDataFrame constructor
AlignedDataFrame-class | (Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
AlignedRead | (Legacy) Construct objects of class "AlignedRead"
AlignedRead-class | (Legacy) "AlignedRead" class for aligned short reads
alignQuality | (Legacy) Accessors for ShortRead classes
alignQualityFilter | Functions for user-created and built-in ShortRead filters
alphabet-method | Quality scores for short reads and their alignments
alphabetByCycle | Summarize nucleotide, amino acid, or quality scores by cycle
alphabetByCycle-method | Quality scores for short reads and their alignments
alphabetByCycle-method | "ShortRead" class for short reads
alphabetByCycle-method | "ShortReadQ" class for short reads and their quality scores
alphabetByCycle-method | Summarize nucleotide, amino acid, or quality scores by cycle
alphabetFrequency-method | Quality scores for short reads and their alignments
alphabetScore | Efficiently calculate the sum of quality scores across bases
alphabetScore-method | Quality scores for short reads and their alignments
alphabetScore-method | "ShortReadQ" class for short reads and their quality scores
analysisPath | (Legacy) Accessors for ShortRead classes
annTrack | Class '"Snapshot"'
annTrack-method | Class '"Snapshot"'
append-method | (Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
append-method | (Legacy) "AlignedRead" class for aligned short reads
append-method | Quality scores for short reads and their alignments
append-method | "ShortRead" class for short reads
append-method | FASTQ input and manipulation.
append-method | "ShortReadQ" class for short reads and their quality scores
ArrayIntensity | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
ArrayIntensity-class | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

## -- B --

baseCallPath | (Legacy) Accessors for ShortRead classes
basePath | Deprecated and defunct functions
BowtieQA-class | (Legacy) Quality assessment summaries from Bowtie files

## -- C --

c-method | "SRFilter" for representing functions operating on ShortRead objects
chromosome | (Legacy) Accessors for ShortRead classes
chromosome-method | (Legacy) "AlignedRead" class for aligned short reads
chromosomeFilter | Functions for user-created and built-in ShortRead filters
clean | Remove sequences with ambiguous nucleotides from short read classes
clean-method | "ShortRead" class for short reads
clean-method | Remove sequences with ambiguous nucleotides from short read classes
close.ShortReadFile | Sampling and streaming records from fastq files
coerce-method | (Legacy) "AlignedRead" class for aligned short reads
coerce-method | Quality scores for short reads and their alignments
coerce-method | "SRFilter" for representing functions operating on ShortRead objects
coerce-method | "ShortRead" class for short reads
coerce-method | "ShortReadQ" class for short reads and their quality scores
compose | Functions for user-created and built-in ShortRead filters
countFastq | Read, write, and count records in FASTQ-formatted files
countFastq-method | Sampling and streaming records from fastq files
countFastq-method | Read, write, and count records in FASTQ-formatted files
countLines | Count lines in all (text) files in a directory whose file name matches a pattern
coverage-method | (Legacy) "AlignedRead" class for aligned short reads

## -- D --

dataPath | (Legacy) Accessors for ShortRead classes
defunct | Deprecated and defunct functions
deprecated | Deprecated and defunct functions
detail-method | (Legacy) "AlignedRead" class for aligned short reads
detail-method | (Legacy) "ExperimentPath" class representing a file hierarchy of data files
detail-method | Quality scores for short reads and their alignments
detail-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
detail-method | (Legacy) A base class for Roche experiment-wide data
detail-method | ".SRUtil" and related classes
detail-method | "ShortRead" class for short reads
detail-method | "ShortReadQ" class for short reads and their quality scores
detail-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
detail-method | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
dim-method | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
dim-method | Quality scores for short reads and their alignments
dustyFilter | Functions for user-created and built-in ShortRead filters
dustyScore | Summarize low-complexity sequences
dustyScore-method | Summarize low-complexity sequences

## -- E --

encoding-method | Quality scores for short reads and their alignments
ExperimentPath | (Legacy) "ExperimentPath" class representing a file hierarchy of data files
experimentPath | (Legacy) Accessors for ShortRead classes
ExperimentPath-class | (Legacy) "ExperimentPath" class representing a file hierarchy of data files
experimentPath-method | (Legacy) A base class for Roche experiment-wide data

## -- F --

fac | Class '"Snapshot"'
fac-method | Class '"Snapshot"'
FastqFile | Sampling and streaming records from fastq files
FastqFile-class | Sampling and streaming records from fastq files
FastqFileList | Sampling and streaming records from fastq files
FastqFileList-class | Sampling and streaming records from fastq files
FastqFileList-method | Sampling and streaming records from fastq files
FastqFileReader-class | Sampling and streaming records from fastq files
FastqQA | Quality assessment of fastq files and ShortReadQ objects
FastqQA-class | Quality assessment of fastq files and ShortReadQ objects
FastqQuality | Construct objects indicating read or alignment quality
FastqQuality-class | Quality scores for short reads and their alignments
FastqQuality-method | Construct objects indicating read or alignment quality
FastqSampler | Sampling and streaming records from fastq files
FastqSampler-class | Sampling and streaming records from fastq files
FastqSamplerList | Sampling and streaming records from fastq files
FastqSamplerList-class | Sampling and streaming records from fastq files
FastqSamplerList-method | Sampling and streaming records from fastq files
FastqStreamer | Sampling and streaming records from fastq files
FastqStreamer-class | Sampling and streaming records from fastq files
FastqStreamer-method | Sampling and streaming records from fastq files
FastqStreamerList | Sampling and streaming records from fastq files
FastqStreamerList-class | Sampling and streaming records from fastq files
FastqStreamerList-method | Sampling and streaming records from fastq files
files | Class '"Snapshot"'
files-method | Class '"Snapshot"'
filterFastq | Filter fastq from one file to another
flag | (Updated) quality assessment reports on short reads
flag-method | (Updated) quality assessment reports on short reads
functions | Class '"Snapshot"'
functions-method | Class '"Snapshot"'

## -- G --

getTrellis | Class '"Snapshot"'
getTrellis-method | Class '"Snapshot"'

## -- I --

id | "ShortRead" class for short reads
id-method | "ShortRead" class for short reads
idFilter | Functions for user-created and built-in ShortRead filters
ignore.strand | Class '"Snapshot"'
ignore.strand-method | Class '"Snapshot"'
imageAnalysisPath | (Legacy) Accessors for ShortRead classes
IntegerQuality | Construct objects indicating read or alignment quality
IntegerQuality-class | Quality scores for short reads and their alignments
intensity | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
Intensity-class | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
IntensityInfo-class | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
IntensityMeasure-class | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

## -- L --

laneDescription | (Legacy) Accessors for ShortRead classes
laneNames | (Legacy) Accessors for ShortRead classes
laneNames-method | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
lapply-method | ".SRUtil" and related classes
left | Class "SpTrellis"
left-method | Class "SpTrellis"
length-method | Quality scores for short reads and their alignments
length-method | ".SRUtil" and related classes
length-method | "ShortRead" class for short reads
limits | Class "SnapshotFunction"
Logic-method | "SRFilterResult" for SRFilter output and statistics

## -- M --

MAQMapQA | (Legacy) Quality assessment summaries from MAQ map files
MAQMapQA-class | (Legacy) Quality assessment summaries from MAQ map files
MatrixQuality | Construct objects indicating read or alignment quality
MatrixQuality-class | Quality scores for short reads and their alignments
measurementError | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

## -- N --

name | "SRFilter" for representing functions operating on ShortRead objects
name-method | "SRFilter" for representing functions operating on ShortRead objects
name-method | "SRFilterResult" for SRFilter output and statistics
names-method | ".SRUtil" and related classes
names<--method | ".SRUtil" and related classes
narrow-method | Quality scores for short reads and their alignments
narrow-method | "ShortRead" class for short reads
narrow-method | "ShortReadQ" class for short reads and their quality scores
nFilter | Functions for user-created and built-in ShortRead filters
NumericQuality | Construct objects indicating read or alignment quality
NumericQuality-class | Quality scores for short reads and their alignments

## -- O --

occurrenceFilter | Functions for user-created and built-in ShortRead filters
open.ShortReadFile | Sampling and streaming records from fastq files

## -- P --

pan | Class '"Snapshot"'
pan-method | Class '"Snapshot"'
phenoData-method | (Legacy) A base class for Roche experiment-wide data
polyn | Utilities for common, simple operations
polynFilter | Functions for user-created and built-in ShortRead filters
position | (Legacy) Accessors for ShortRead classes
position-method | (Legacy) "AlignedRead" class for aligned short reads
positionFilter | Functions for user-created and built-in ShortRead filters

## -- Q --

QA | (Updated) quality assessment reports on short reads
qa | Perform quality assessment on short reads
QA-class | (Updated) classes for representing quality assessment results
qa-method | "ShortReadQ" class for short reads and their quality scores
qa-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
qa-method | Perform quality assessment on short reads
qa2 | (Updated) quality assessment reports on short reads
qa2-method | (Updated) quality assessment reports on short reads
QAAdapterContamination | (Updated) quality assessment reports on short reads
QAAdapterContamination-class | (Updated) classes for representing quality assessment results
QACollate | (Updated) quality assessment reports on short reads
QACollate-class | (Updated) classes for representing quality assessment results
QACollate-method | (Updated) quality assessment reports on short reads
QAData | (Updated) quality assessment reports on short reads
QAData-class | (Updated) classes for representing quality assessment results
QAFastqSource | (Updated) quality assessment reports on short reads
QAFastqSource-class | (Updated) classes for representing quality assessment results
QAFiltered | (Updated) quality assessment reports on short reads
QAFiltered-class | (Updated) classes for representing quality assessment results
QAFlagged | (Updated) quality assessment reports on short reads
QAFlagged-class | (Updated) classes for representing quality assessment results
QAFrequentSequence | (Updated) quality assessment reports on short reads
QAFrequentSequence-class | (Updated) classes for representing quality assessment results
QANucleotideByCycle | (Updated) quality assessment reports on short reads
QANucleotideByCycle-class | (Updated) classes for representing quality assessment results
QANucleotideUse | (Updated) quality assessment reports on short reads
QANucleotideUse-class | (Updated) classes for representing quality assessment results
QAQualityByCycle | (Updated) quality assessment reports on short reads
QAQualityByCycle-class | (Updated) classes for representing quality assessment results
QAQualityUse | (Updated) quality assessment reports on short reads
QAQualityUse-class | (Updated) classes for representing quality assessment results
QAReadQuality | (Updated) quality assessment reports on short reads
QAReadQuality-class | (Updated) classes for representing quality assessment results
QASequenceUse | (Updated) quality assessment reports on short reads
QASequenceUse-class | (Updated) classes for representing quality assessment results
QASource-class | (Updated) classes for representing quality assessment results
QASummary-class | (Updated) classes for representing quality assessment results
QualityScore-class | Quality scores for short reads and their alignments
qualPath | (Legacy) "RochePath" class representing a Roche (454) experiment location

## -- R --

rbind-method | Virtual class for representing quality assessment results
rbind-method | (Updated) quality assessment reports on short reads
read454 | (Legacy) "RochePath" class representing a Roche (454) experiment location
read454-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
readAligned | (Legacy) Read aligned reads and their quality scores into R representations
readAligned-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readAligned-method | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
readAligned-method | Deprecated and defunct functions
readAligned-method | (Legacy) Read aligned reads and their quality scores into R representations
readBaseQuality | (Legacy) Read short reads and their quality scores into R representations
readBaseQuality-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
readBaseQuality-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readBaseQuality-method | (Legacy) Read short reads and their quality scores into R representations
readBfaToc | (Legacy) Get a list of the sequences in a Maq .bfa file
readCount | (Legacy) A base class for Roche experiment-wide data
readData | (Legacy) A base class for Roche experiment-wide data
reader | Class "SnapshotFunction"
readFasta | Read and write FASTA files to or from ShortRead objects
readFasta-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
readFasta-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readFasta-method | Read and write FASTA files to or from ShortRead objects
readFastaQual | (Legacy) "RochePath" class representing a Roche (454) experiment location
readFastaQual-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
readFastq | Read, write, and count records in FASTQ-formatted files
readFastq-method | Sampling and streaming records from fastq files
readFastq-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readFastq-method | Read, write, and count records in FASTQ-formatted files
readIndex | (Legacy) A base class for Roche experiment-wide data
readIntensities | (Legacy) Read Illumina image intensity files
readIntensities-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readIntensities-method | (Legacy) Read Illumina image intensity files
readIntensityInfo | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
readPath | (Legacy) "RochePath" class representing a Roche (454) experiment location
readPrb | (Legacy) Read Solexa prb files as fastq-style quality scores
readPrb-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readPrb-method | (Legacy) Read Solexa prb files as fastq-style quality scores
readQseq | (Legacy) Read Solexa qseq files as fastq-style quality scores
readQseq-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
readQseq-method | (Legacy) Read Solexa qseq files as fastq-style quality scores
readQual | (Legacy) "RochePath" class representing a Roche (454) experiment location
readQual-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
readXStringColumns | Read one or more columns into XStringSet (e.g., DNAStringSet) objects
renew | Renew (update) a ShortRead object with new values
renew-method | Renew (update) a ShortRead object with new values
renewable | Renew (update) a ShortRead object with new values
renewable-method | Renew (update) a ShortRead object with new values
report | Summarize quality assessment results into a report
report-method | (Legacy) Quality assessment summaries from Bowtie files
report-method | Quality assessment of fastq files and ShortReadQ objects
report-method | (Legacy) Quality assessment summaries from MAQ map files
report-method | (Legacy) Quality assessment summaries from Solexa export and realign files
report-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
report-method | (Updated) quality assessment reports on short reads
report-method | Summarize quality assessment results into a report
report_html | Summarize quality assessment results into a report
report_html-method | (Legacy) Quality assessment summaries from Bowtie files
report_html-method | Quality assessment of fastq files and ShortReadQ objects
report_html-method | (Legacy) Quality assessment summaries from MAQ map files
report_html-method | (Legacy) Quality assessment summaries from Solexa export and realign files
restore | Class "SpTrellis"
restore-method | Class "SpTrellis"
reverse-method | Quality scores for short reads and their alignments
reverse-method | "ShortReadQ" class for short reads and their quality scores
reverseComplement-method | "ShortReadQ" class for short reads and their quality scores
right | Class "SpTrellis"
right-method | Class "SpTrellis"
RochePath | (Legacy) "RochePath" class representing a Roche (454) experiment location
RochePath-class | (Legacy) "RochePath" class representing a Roche (454) experiment location
RocheSet | (Legacy) Roche (454) experiment-wide data container
RocheSet-class | (Legacy) Roche (454) experiment-wide data container
RocheSet-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
RtaIntensity | (Legacy) Construct objects of class "RtaIntensity"
RtaIntensity-class | (Legacy) Class "RtaIntensity"
runNames | (Legacy) "RochePath" class representing a Roche (454) experiment location
runNames-method | (Legacy) "RochePath" class representing a Roche (454) experiment location

## -- S --

sapply-method | ".SRUtil" and related classes
scanPath | (Legacy) Accessors for ShortRead classes
SFastqQuality | Construct objects indicating read or alignment quality
SFastqQuality-class | Quality scores for short reads and their alignments
SFastqQuality-method | Construct objects indicating read or alignment quality
ShortRead | "ShortRead" class for short reads
ShortRead-class | "ShortRead" class for short reads
ShortRead-method | "ShortRead" class for short reads
ShortReadFile-class | Sampling and streaming records from fastq files
ShortReadQ | "ShortReadQ" class for short reads and their quality scores
ShortReadQ-class | "ShortReadQ" class for short reads and their quality scores
ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores
ShortReadQQA-class | Quality assessment of fastq files and ShortReadQ objects
show-method | (Legacy) "AlignedRead" class for aligned short reads
show-method | (Legacy) "ExperimentPath" class representing a file hierarchy of data files
show-method | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
show-method | Quality scores for short reads and their alignments
show-method | (Legacy) "RochePath" class representing a Roche (454) experiment location
show-method | "SRFilter" for representing functions operating on ShortRead objects
show-method | "SRFilterResult" for SRFilter output and statistics
show-method | (Legacy) A base class for Roche experiment-wide data
show-method | ".SRUtil" and related classes
show-method | "ShortRead" class for short reads
show-method | FASTQ input and manipulation.
show-method | Class '"Snapshot"'
show-method | Class "SnapshotFunction"
show-method | (Legacy) Quality assessment summaries from Solexa export and realign files
show-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
show-method | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
show-method | Class "SpTrellis"
show-method | Virtual class for representing quality assessment results
show-method | (Updated) quality assessment reports on short reads
Snapshot | Class '"Snapshot"'
Snapshot-class | Class '"Snapshot"'
Snapshot-method | Class '"Snapshot"'
SnapshotFunction | Class "SnapshotFunction"
SnapshotFunction-class | Class "SnapshotFunction"
SnapshotFunctionList | Class "SnapshotFunction"
SnapshotFunctionList-class | Class "SnapshotFunction"
SnapshotFunctionList-method | Class "SnapshotFunction"
SolexaExportQA | (Legacy) Quality assessment summaries from Solexa export and realign files
SolexaExportQA-class | (Legacy) Quality assessment summaries from Solexa export and realign files
SolexaIntensity | (Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensity-class | Classes "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensityInfo | (Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensityInfo-class | Classes "SolexaIntensity" and "SolexaIntensityInfo"
SolexaPath | (Legacy) "SolexaPath" class representing a standard output file hierarchy
solexaPath | (Legacy) Accessors for ShortRead classes
SolexaPath-class | (Legacy) "SolexaPath" class representing a standard output file hierarchy
SolexaRealignQA-class | (Legacy) Quality assessment summaries from Solexa export and realign files
SolexaSet | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
SolexaSet-class | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
SolexaSet-method | (Legacy) "SolexaPath" class representing a standard output file hierarchy
SolexaSet-method | (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
sourcePath | (Legacy) A base class for Roche experiment-wide data
SpTrellis | Class "SpTrellis"
SpTrellis-class | Class "SpTrellis"
spViewPerFeature | Tools to visualize genomic data
srapply | Deprecated and defunct functions
srdistance | Edit distances between reads and a small number of short references
srdistance-method | "ShortRead" class for short reads
srdistance-method | Edit distances between reads and a small number of short references
srdistanceFilter | Functions for user-created and built-in ShortRead filters
srduplicated | Order, sort, and find duplicates in XStringSet objects
srduplicated-method | (Legacy) "AlignedRead" class for aligned short reads
srduplicated-method | Quality scores for short reads and their alignments
srduplicated-method | "ShortRead" class for short reads
srduplicated-method | Order, sort, and find duplicates in XStringSet objects
sread | "ShortRead" class for short reads
sread-method | "ShortRead" class for short reads
SRError | ".SRUtil" and related classes
SRError-class | ".SRUtil" and related classes
srFilter | Functions for user-created and built-in ShortRead filters
SRFilter-class | "SRFilter" for representing functions operating on ShortRead objects
srFilter-method | "SRFilter" for representing functions operating on ShortRead objects
srFilter-method | Functions for user-created and built-in ShortRead filters
SRFilterResult | "SRFilterResult" for SRFilter output and statistics
SRFilterResult-class | "SRFilterResult" for SRFilter output and statistics
SRList | ".SRUtil" and related classes
srlist | ".SRUtil" and related classes
SRList-class | ".SRUtil" and related classes
srorder | Order, sort, and find duplicates in XStringSet objects
srorder-method | (Legacy) "AlignedRead" class for aligned short reads
srorder-method | Quality scores for short reads and their alignments
srorder-method | "ShortRead" class for short reads
srorder-method | Order, sort, and find duplicates in XStringSet objects
srrank | Order, sort, and find duplicates in XStringSet objects
srrank-method | (Legacy) "AlignedRead" class for aligned short reads
srrank-method | Quality scores for short reads and their alignments
srrank-method | "ShortRead" class for short reads
srrank-method | Order, sort, and find duplicates in XStringSet objects
SRSet-class | (Legacy) A base class for Roche experiment-wide data
srsort | Order, sort, and find duplicates in XStringSet objects
srsort-method | Quality scores for short reads and their alignments
srsort-method | "ShortRead" class for short reads
srsort-method | Order, sort, and find duplicates in XStringSet objects
SRVector | ".SRUtil" and related classes
SRVector-class | ".SRUtil" and related classes
SRWarn | ".SRUtil" and related classes
SRWarn-class | ".SRUtil" and related classes
stats | "SRFilterResult" for SRFilter output and statistics
stats-method | "SRFilterResult" for SRFilter output and statistics
strand-method | (Legacy) "AlignedRead" class for aligned short reads
strandFilter | Functions for user-created and built-in ShortRead filters

## -- T --

tables | Summarize XStringSet read frequencies
tables-method | "ShortRead" class for short reads
tables-method | Summarize XStringSet read frequencies
togglefun | Class '"Snapshot"'
togglefun-method | Class '"Snapshot"'
togglep | Class '"Snapshot"'
togglep-method | Class '"Snapshot"'
togglez | Class '"Snapshot"'
togglez-method | Class '"Snapshot"'
trellis-class | Class '"Snapshot"'
trimEnds | Trim ends of reads based on nucleotides or qualities
trimEnds-method | Trim ends of reads based on nucleotides or qualities
trimLRPatterns-method | "ShortRead" class for short reads
trimTails | Trim ends of reads based on nucleotides or qualities
trimTails-method | Quality scores for short reads and their alignments
trimTails-method | "ShortReadQ" class for short reads and their quality scores
trimTails-method | Trim ends of reads based on nucleotides or qualities
trimTailw | Trim ends of reads based on nucleotides or qualities
trimTailw-method | Quality scores for short reads and their alignments
trimTailw-method | "ShortReadQ" class for short reads and their quality scores
trimTailw-method | Trim ends of reads based on nucleotides or qualities

## -- U --

uniqueFilter | Deprecated functions from the ShortRead package

## -- V --

vclass | (Legacy) Accessors for ShortRead classes
view | Class '"Snapshot"'
view-method | Class '"Snapshot"'
viewer | Class "SnapshotFunction"
vrange | Class '"Snapshot"'
vrange-method | Class '"Snapshot"'

## -- W --

width-method | Quality scores for short reads and their alignments
width-method | "ShortRead" class for short reads
writeFasta | Read and write FASTA files to or from ShortRead objects
writeFasta-method | "ShortRead" class for short reads
writeFasta-method | Read and write FASTA files to or from ShortRead objects
writeFastq | Read, write, and count records in FASTQ-formatted files
writeFastq-method | "ShortReadQ" class for short reads and their quality scores

## -- Y --

yield | Sampling and streaming records from fastq files
yield-method | Sampling and streaming records from fastq files

## -- Z --

zi | Class "SpTrellis"
zi-method | Class "SpTrellis"
zo | Class "SpTrellis"
zo-method | Class "SpTrellis"
zoom | Class '"Snapshot"'
zoom-method | Class '"Snapshot"'

## -- misc --

!-method | "SRFilterResult" for SRFilter output and statistics
%in%-method | (Legacy) "AlignedRead" class for aligned short reads
.QA-class | Virtual class for representing quality assessment results
.QA2-class | (Updated) classes for representing quality assessment results
.Roche-class | FASTQ input and manipulation.
.ShortReadBase-class | FASTQ input and manipulation.
.Solexa-class | FASTQ input and manipulation.
.SRUtil-class | ".SRUtil" and related classes
[-method | (Legacy) "AlignedRead" class for aligned short reads
[-method | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[-method | Quality scores for short reads and their alignments
[-method | ".SRUtil" and related classes
[-method | "ShortRead" class for short reads
[-method | "ShortReadQ" class for short reads and their quality scores
[-method | Classes "SolexaIntensity" and "SolexaIntensityInfo"
[<--method | "ShortReadQ" class for short reads and their quality scores
[[-method | (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
[[-method | Quality scores for short reads and their alignments
[[-method | ".SRUtil" and related classes