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.
BactSNP has two modes: Assembly mode and Mapping mode. For now, we recommend Assembly Mode (default), because the realignment step in Mapping mode is time-consuming.
Most modules are precompiled for Linux 64bit systems. Some modules still need to be compiled, but tools which need to be pre-installed are fewer than bactsnp_v1.0.0_src.tgz.
Users can compile all submodules.
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 in both mode.
- In Mapping mode, BactSNP detects repetitive regions in the reference genome automatically. However, this is only a simple function, so we recommend to specify repetitive regions (e.g. rRNA, IS (Insertion Sequence)) manually with –mask_region option.