@@ 5308,6 5308,48 @@ microarray data. A variety of basic manipulation tools for graphs, hypothesis
testing and other simple calculations.")
(license license:artistic2.0)))
+(define-public r-shortread
+ (package
+ (name "r-shortread")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ShortRead" version))
+ (sha256
+ (base32
+ "0qlxns4bhwfpafx3km2lnivgl2qyp7n4g1ardm6vrinpq8paxbjg"))))
+ (properties `((upstream-name . "ShortRead")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "http://bioconductor.org/packages/ShortRead")
+ (synopsis "FASTQ input and manipulation tools")
+ (description
+ "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report. Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes. The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")