Metadata-Version: 2.1
Name: snipgenie
Version: 0.7.0
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
Keywords: bioinformatics,biology,genomics
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
Requires-Dist: numpy>=1.2
Requires-Dist: pandas>=0.24
Requires-Dist: matplotlib>=3.0
Requires-Dist: biopython==1.84
Requires-Dist: pyvcf3
Requires-Dist: pyfaidx
Requires-Dist: bcbio_gff
Requires-Dist: tqdm

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
* 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
