snp-mutator 1.2.0

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.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.

History

1.2.0 (2019-05-15)

• Added support for Python 3.6 and 3.7.

• Added a command line option to specify the output directory for the generated fasta files.

1.1.0 (2018-10-23)

• Added the capability to specify the fasta defline sequence id in the output files.

• The unmutated, but concatenated sequence reference can be written to a separate output file. All the replicates will be mutations of this file.

1.0.0 (2018-10-12)

• 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.

• Mutations can be either monomorphic or polymorphic.

• Add the capability to generate VCF output files.

• Add the capability to generate a metrics output file.

• The installer creates an executable script called snpmutator.

• Insertions are now placed after the original reference position, not before, as in prior versions of snpmutator. This means it will not be possible to exactly reproduce the results of prior versions of this software.

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.