SNP Mutator

Generate mutated sequence files from a reference genome.

SNP Mutator was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition.

• Free software
• Documentation: https://snp-mutator.readthedocs.io/en/latest/readme.html
• Source Code: https://github.com/CFSAN-Biostatistics/snp-mutator
• PyPI Distribution: https://pypi.python.org/pypi/snp-mutator

Features

• Reads a fasta file and generates any number of mutated fasta replicate files.
• Mutations can be any number of single-base substitutions, insertions, and deletions at randomly chosen positions, uniformly distributed across the genome.
• Mutations can be chosen from a subset (pool) of all possible positions.
• Replicates can be partitioned into multiple groups with each group sharing a pool of eligible positions.
• Generates a summary file listing the original base and the mutation for all mutated positions.
• Mutations can be either monomorphic or polymorphic.
• VCF file generation.
• Various metrics can be saved to an output file.
• The fasta defline sequence id can be customized.

Citing SNP Mutator

To cite SNP Mutator, please cite the publication below:

Davis S, Pettengill JB, Luo Y, Payne J, Shpuntoff A, Rand H, Strain E. (2015) CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20 https://doi.org/10.7717/peerj-cs.20

License

See the LICENSE file included in the SNP Mutator distribution.