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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. Anyone interested in using the software is encouraged to make suggestions on improving or adding features.
This software is written in Python. It was developed on Ubuntu Linux but can also run on Windows 10 via WSL. Linux is recommended. The GUI is made using the Qt toolkit using PyQt5/PySide2.
- load multiple fastq files and process together
- view fastq quality statistics
- trim reads
- align to reference (fasta file with single chromosome)
- view bam alignments
- call variants
- filter variants
- create SNP core multiple sequence alignment