recipe bioconductor-basecallqc

Working with Illumina Basecalling and Demultiplexing input and output files

Homepage

https://bioconductor.org/packages/3.11/bioc/html/basecallQC.html

License

GPL (>= 3)

Recipe

/bioconductor-basecallqc/meta.yaml

The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

package bioconductor-basecallqc

(downloads) docker_bioconductor-basecallqc

Versions

1.12.0-0, 1.10.0-0, 1.8.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0

Depends
Required By

Installation

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

conda install bioconductor-basecallqc

and update with:

conda update bioconductor-basecallqc

or use the docker container:

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

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

Notes

‘This package relies on bcl2fastq being available in the system PATH. Due to licensing restrictions Bioconda does not provide this package.’