recipe bioconductor-rfastp

An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

Homepage

https://bioconductor.org/packages/3.14/bioc/html/Rfastp.html

License

GPL-3 + file LICENSE

Recipe

/bioconductor-rfastp/meta.yaml

Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.

package bioconductor-rfastp

Versions

1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

Depends

• bioconductor-rhtslib >=1.26.0,<1.27.0

• 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

• r-ggplot2

• r-rcpp

• r-reshape2

• r-rjson

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-rfastp

and update with:

conda update bioconductor-rfastp

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-rfastp:<tag>

(see bioconductor-rfastp/tags for valid values for <tag>)

Download stats

Link to this page

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