confil

🚫 🚧 For in-house use

confil parses a kraken2 report and determines contamination based on a specified cutoff.

Requirements

• kraken2

Up and running

$ git clone https://github.com/COMBAT-TB/confil.git
...
$ cd confil
$ virtualenv envname
$ source envname/bin/activate
$ pip install -r requirements.txt
$ python setup.py install
$ confil --help
$ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq