Metadata-Version: 1.1
Name: snipgenie
Version: 0.4.0
Summary: variant calling and phylogenies from microbial WGS data
Home-page: https://github.com/dmnfarrell/snipgenie
Author: Damien Farrell
Author-email: farrell.damien@gmail.com
License: GPL v3
Description: Background
        ----------
        
        SNiPgenie is a tool for microbial variant calling and phylogenetic analysis from
        raw read data. It was primarily written to be used with bacterial isolates of M. bovis
        but can be applied to other species. You need a good quality reference genome to align to.
        
        Dependencies
        ------------
        
        numpy
        pandas
        biopython
        matplotlib
        future
        pyvcf
        pyfaidx
        bcbio_gff
        pyside2 (for gui only)
        
        Other binaries required:
        
        * bwa
        * samtools
        * bcftools
        * tabix
        * parallel
        
        These binaries can be installed with apt in Ubuntu:
        
        `sudo apt install bwa samtools bcftools tabix parallel`
        
        Installation
        ------------
        
        From pypi::
        
          pip install snipgenie
        
        From github::
        
          pip install -e git+https://github.com/dmnfarrell/snipgenie.git#egg=snipgenie
        
        Usage
        -----
        
        Call with your own reference fasta file::
        
          snipgenie -r reference.fa -i data_files -o results
        
        Use an in built species genome as reference. This will also supply an annotation file.
        The current options are `Mbovis-AF212297, MTB-H37Rv, MAP-K10, M.smegmatis-MC2155`::
        
          snipgenie -S Mbovis-AF212297 -i data_files -o results
        
        
        Provide more than one folder::
        
          snipgenie -r reference.fa -i data_files1 -i data_files2 -o results
        
        
        Provide an annotation (genbank format) for consequence calling::
        
          snipgenie -r reference.fa -g reference.gb -i data_files -o results
        
        Add your own filters and provide threads::
        
          snipgenie -r reference.fa -i data_files -t 8 -o results` \
          -f 'QUAL>=40 && INFO/DP>=20 && MQ>40'
        
        Links
        -----
        
        * https://github.com/dmnfarrell/snipgenie
        
Keywords: bioinformatics,biology,genomics
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
