Metadata-Version: 1.1
Name: chfilter
Version: 1.3
Summary: Simple instructions to remove 16s rRNA reads from metagenomics samples
Home-page: https://github.com/gaarangoa/chfilter
Author: Gustavo Arango
Author-email: gustavo1@vt.edu
License: BSD-2
Description-Content-Type: UNKNOWN
Description: ## Chloroplast removal tool
        
        This is a simple tool that removes all 16s rRNAs-like reads from a paired-end sample. By using Bowtie2 paired end reads are screened against the 16S-rRNAs from the greengenes database and removed from the samples. 
        
        ### Requirements
        Make sure you have installed the following software (packages):
            Bowtie2
        <!-- BioPython -->
        
        ### Instalation
        
            pip install chfilter --user
        
        <!-- python setup.py install -->
        <!-- pip install . --upgrade -->
        
        ### Usage
            usage: chfiler remove [-h] --paired-1 PAIRED_1 --paired-2 PAIRED_2 --out-dir OUT_DIR
        
            optional arguments:
            -h, --help           show this help message and exit
            --paired-1 PAIRED_1  paired read 1
            --paired-2 PAIRED_2  paired read 2
            --out-dir OUT_DIR    output directory
        
        #### Usage example
            clremove clear --paired-1 ./test/r1.fq --paired-2 ./test/r2.fq --out-dir ./test/
        
        ### output files
        The files with filtered chloroplast reads are stored as 
            
            *.no-chl.fastq
        
Keywords: metagenomics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
