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