rSFFreader: rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers

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rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.

Author
Matt Settles <mattsettles@gmail.com>, Sam Hunter, Brice Sarver, Ilia Zhbannikov, Kyu-Chul Cho
Date of publication
None
Maintainer
Matt Settles <mattsettles@gmail.com>
License
Artistic-2.0
Version
0.22.0

View on Bioconductor

Man pages

availableClipModes
availableClipModes
load454SampleData
Load the example 454 dataset
loadIonSampleData
Load the example Ion Torrent dataset
readsff
Read SFF-formatted files into SffReads or SffReadsQ objects
readsffgeometry
Read in basic statistics about an sff file
readsffheader
Read in sff header
rSFFreader-internals
rSFFreader internals
rSFFreader-package
Base classes and methods for high-throughput sequence data...
SffHeader-class
'SffHeader'
SffReads-class
Class '"SffReads"'. A class for next generation reads stored...
SffReadsQ-class
Class '"SffReadsQ"' for next generation reads stored in SFF...

Files in this package

rSFFreader/.BBSoptions
rSFFreader/DESCRIPTION
rSFFreader/NAMESPACE
rSFFreader/NEWS
rSFFreader/R
rSFFreader/R/allClasses.R
rSFFreader/R/allGenerics.R
rSFFreader/R/methods-Misc.R
rSFFreader/R/methods-SffHeader.R
rSFFreader/R/methods-SffReads.R
rSFFreader/R/methods-SffReadsQ.R
rSFFreader/R/readSFF.R
rSFFreader/README.md
rSFFreader/build
rSFFreader/build/vignette.rds
rSFFreader/inst
rSFFreader/inst/doc
rSFFreader/inst/doc/rSFFreader.R
rSFFreader/inst/doc/rSFFreader.Rnw
rSFFreader/inst/doc/rSFFreader.pdf
rSFFreader/inst/extdata
rSFFreader/inst/extdata/Small454Test.sff
rSFFreader/inst/extdata/SmallTorrentTest.sff
rSFFreader/man
rSFFreader/man/SffHeader-class.Rd
rSFFreader/man/SffReads-class.Rd
rSFFreader/man/SffReadsQ-class.Rd
rSFFreader/man/availableClipModes.Rd
rSFFreader/man/load454SampleData.Rd
rSFFreader/man/loadIonSampleData.Rd
rSFFreader/man/rSFFreader-internals.Rd
rSFFreader/man/rSFFreader-package.Rd
rSFFreader/man/readsff.Rd
rSFFreader/man/readsffgeometry.Rd
rSFFreader/man/readsffheader.Rd
rSFFreader/src
rSFFreader/src/Biostrings_stubs.c
rSFFreader/src/IRanges_stubs.c
rSFFreader/src/Makevars.win
rSFFreader/src/R_init_rSFFreader.c
rSFFreader/src/S4Vectors_stubs.c
rSFFreader/src/SFF-io.c
rSFFreader/src/XVector_stubs.c
rSFFreader/src/rSFFreader.h
rSFFreader/vignettes
rSFFreader/vignettes/rSFFreader.Rnw