BactSNP is a tool to identify SNPs among bacterial isolates. BactSNP can detect SNPs and create a simple TSV file with SNP information as well as an alignment FASTA file containing reconstructed pseudo-genomes of the target isolates in a one-step process.
Some modules still need to be compiled, but most modules are precompiled for Linux 64bit systems.
Please read bactsnp_<version>/others/REQUIREMENTS.
Please read bactsnp_<version>/others/INSTALL.
Prepare <in.fastq_list> following bactsnp_<version>/others/fq_list_format and execute the command below.
> bactsnp -f <in.fastq_list> -r <in.reference.fasta> -o <output directory>
Please read bactsnp_<version>/README for full usage instructions.
Please read bactsnp_<version>/README for the description of each output file or directory.
- We recommend coverage depth of at least 30x.
- BactSNP is capable of accurate SNP calling by default, but in order to make it more accurate, we recommend to specify repetitive regions (e.g. rRNA, IS (Insertion Sequence)) manually with –mask_region
- For phylogenetic analysis, we recommend to use Gubbins (https://www.sanger.ac.uk/science/tools/gubbins). Gubbins identifies recombination regions containing an elevated density of SNPs statistically and construct a phylogenetic tree using SNPs outside those regions. The outputs of BactSNP replaced_pseudo_genomes_*_ref.fa can be input to Gubbins