recipe biopet-extractadaptersfastqc

ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report.

Homepage

https://github.com/biopet/extractadaptersfastqc

License

MIT

Recipe

/biopet-extractadaptersfastqc/meta.yaml

ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report. These sequences can be used as input for a QC tool such as cutadapt. The sequences can be output in plain text format with a newline character as a separator between the sequences. Alternatively the sequences can be output in FASTA format.

For documentation and manuals visit our github.io page: https://biopet.github.io/extractadaptersfastqc

package biopet-extractadaptersfastqc

(downloads) docker_biopet-extractadaptersfastqc

Versions

0.2-1, 0.2-0, 0.1-1, 0.1-0

Depends
Required By

Installation

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

conda install biopet-extractadaptersfastqc

and update with:

conda update biopet-extractadaptersfastqc

or use the docker container:

docker pull quay.io/biocontainers/biopet-extractadaptersfastqc:<tag>

(see biopet-extractadaptersfastqc/tags for valid values for <tag>)

Notes

biopet-extractadaptersfastqc is a Java program that comes with a custom wrapper shell script. By default ‘no default java option’ is set in the wrapper. The command that runs the program is ‘biopet-extractadaptersfastqc’. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ‘biopet-extractadaptersfastqc -Xms512m -Xmx1g’.