snp-mutator 0.2.0

Generate mutated sequence files from a reference genome.

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.org.

• 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.

• Generates a summary file listing the original base and the mutation for all mutated positions.

Citing SNP Mutator

To cite SNP Mutator, please reference the SNP Mutator GitHub repository:

https://github.com/CFSAN-Biostatistics/snp-mutator

License

See the LICENSE file included in the SNP Mutator distribution.

History

0.2.0 (2016-01-15)

• Allow lowercase bases in the input fasta file.

• Do not mutate gaps or ambiguous positions.

• Add a command line switch to show the program version.

0.1.1 (2015-06-17)

• Remove spaces from the summary file column headings. This will simplify downstream analysis in some scripting languages.

0.1.0 (2015-05-21)

• First release on GitHub, Read the Docs, and PyPI.