- recipe bioconductor-shortread
FASTQ input and manipulation
- Homepage:
https://bioconductor.org/packages/3.16/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:
1.56.0-1
,1.56.0-0
,1.52.0-2
,1.52.0-1
,1.52.0-0
,1.50.0-0
,1.48.0-1
,1.48.0-0
,1.46.0-0
,1.56.0-1
,1.56.0-0
,1.52.0-2
,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
>=2.58.0,<2.59.0
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-biocparallel
>=1.32.0,<1.33.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicalignments
>=1.34.0,<1.35.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-rhtslib
>=2.0.0,<2.1.0
bioconductor-rsamtools
>=2.14.0,<2.15.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-xvector
>=0.38.0,<0.39.0
bioconductor-zlibbioc
>=1.44.0,<1.45.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see 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)