Mercurial > repos > sanbi-uwc > confil
view confil.egg-info/PKG-INFO @ 10:2cde7c81c694 draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 036172521321dbafe62e6d72b3a491f4bc4b9dc9-dirty
author | sanbi-uwc |
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date | Fri, 08 Mar 2019 12:46:23 -0500 |
parents | 3892ea8ad1ad |
children | 5ec97cccb3fe |
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Metadata-Version: 2.1 Name: confil Version: 0.1.3.dev20190307 Summary: Contamination filter Home-page: https://github.com/COMBAT-TB/confil License: UNKNOWN Description: # confil [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil) [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil) :no_entry_sign: :construction: **For in-house use** `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff. ## Requirements - kraken2 ## Up and running ```sh $ 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 ``` Keywords: contamination,filter Platform: UNKNOWN Description-Content-Type: text/markdown