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
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