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/3.16/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:

1.8.0-1,  1.8.0-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

Depends:

• bioconductor-rhtslib >=2.0.0,<2.1.0

• 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

• r-ggplot2

• r-rcpp

• r-reshape2

• r-rjson

Required By:

Installation

With an activated Bioconda channel (see 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

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rfastp/README.html)