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
