- recipe bioconductor-shortread
FASTQ input and manipulation
- Homepage
https://bioconductor.org/packages/3.14/bioc/html/ShortRead.html
- License
Artistic-2.0
- Recipe
- Links
biotools: shortread
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.
- package bioconductor-shortread¶
-
- Versions
1.52.0-1
,1.52.0-0
,1.50.0-0
,1.48.0-1
,1.48.0-0
,1.46.0-0
,1.44.0-0
,1.42.0-1
,1.40.0-0
,1.52.0-1
,1.52.0-0
,1.50.0-0
,1.48.0-1
,1.48.0-0
,1.46.0-0
,1.44.0-0
,1.42.0-1
,1.40.0-0
,1.38.0-0
,1.36.0-0
,1.34.2-0
,1.32.0-0
,1.28.0-0
- Depends
bioconductor-biobase
>=2.54.0,<2.55.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicalignments
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rhtslib
>=1.26.0,<1.27.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-xvector
>=0.34.0,<0.35.0
bioconductor-zlibbioc
>=1.40.0,<1.41.0
libblas
>=3.8.0,<4.0a0
libgcc-ng
>=10.3.0
liblapack
>=3.8.0,<4.0a0
libstdcxx-ng
>=10.3.0
r-base
>=4.1,<4.2.0a0
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-shortread
and update with:
conda update bioconductor-shortread
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-shortread:<tag>
(see bioconductor-shortread/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-shortread/README.html)