bioconductor-shortread

Summary

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.

Versions

  • 1.28.0

License

Artistic-2.0

Meta

package:
  name: bioconductor-shortread
  version: 1.28.0
source:
  fn: ShortRead_1.28.0.tar.gz
  url: https://bioarchive.galaxyproject.org/ShortRead_1.28.0.tar.gz
  md5: 94fdda7c3c1d398626e135fa613062f0
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
requirements:
  build:
    - bioconductor-biobase
    - bioconductor-biocparallel    
    - 'bioconductor-biocgenerics >=0.11.3'
    - 'bioconductor-biostrings >=2.37.1'
    - 'bioconductor-genomeinfodb >=1.1.19'
    - 'bioconductor-genomicalignments >=1.5.4'
    - 'bioconductor-genomicranges >=1.21.6'
    - 'bioconductor-iranges >=2.3.7'
    - 'bioconductor-rsamtools >=1.21.4'
    - 'bioconductor-s4vectors >=0.7.1'
    - bioconductor-zlibbioc
    - r
    - r-hwriter
    - r-latticeextra
  run:
    - bioconductor-biobase
    - bioconductor-biocparallel    
    - 'bioconductor-biocgenerics >=0.11.3'
    - 'bioconductor-biostrings >=2.37.1'
    - 'bioconductor-genomeinfodb >=1.1.19'
    - 'bioconductor-genomicalignments >=1.5.4'
    - 'bioconductor-genomicranges >=1.21.6'
    - 'bioconductor-iranges >=2.3.7'
    - 'bioconductor-rsamtools >=1.21.4'
    - 'bioconductor-s4vectors >=0.7.1'
    - bioconductor-zlibbioc
    - r
    - r-hwriter
    - r-latticeextra
test:
  commands:
    - '$R -e "library(''ShortRead'')"'
about:
  home: http://bioconductor.org/packages/release/bioc/html/ShortRead.html
  license: Artistic-2.0
  summary: '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.'