snipgenie 0.6.0

variant calling and phylogenies from microbial WGS data

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