FDSTools: Forensic DNA Sequencing Tools

FDSTools is a package of data analysis tools for Next Generation Sequencing of forensic DNA markers, including tools for characterisation and filtering of PCR stutter artefacts and other systemic noise, and for automatic detection of the alleles in a sample. The software package is written in Python and runs on Windows, Linux or MacOS. Please refer to the User Guide for installation instructions.

FDSTools v2.1 is out!

Get ready for the latest version of FDSTools. In FDSTools v2.1, allele nomenclature is based on STRNaming v1.2. For human targets, no manual configuration of the repeat structure is required anymore. And no manual configuration is required at all if you're using one of the built-in kits. Furthermore, this version contains great improvements regarding microhaplotype loci.

Please refer to the User Guide if you are upgrading from an FDSTools v1.x installation. And please note the information about STRNaming updates when upgrading from FDSTools v2.0 to v2.1. Finally, find more information about FDSTools updates in the Release Notes.

References

Below are some links to resources available elsewhere.

• FDSTools is thoroughly introduced in our article:
  Hoogenboom, J., van der Gaag, K. J., de Leeuw, R. H., Sijen, T., de Knijff, P., and Laros, J. F. FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise. Forensic Sci Int Genet, 27 (2016), 27–40. doi.org/10.1016/j.fsigen.2016.11.007
• The STRNaming STR allele nomenclature system is introduced in:
  Hoogenboom, J., Sijen, T., and van der Gaag, K. J. STRNaming: Generating simple, informative names for sequenced STR alleles in a standardised and automated manner. Forensic Sci Int Genet, 52 (2021), 102473. doi.org/10.1016/j.fsigen.2021.102473
• This article is about the advancements made in FDSTools v2.0 and STRNaming v1.1:
  Hoogenboom, J. Weiler, N. Busscher, L., Struik, L., Sijen, T., and van der Gaag, K. J. Advancing FDSTools by integrating STRNaming 1.1. Forensic Sci Int Genet, 61 (2022), 102768. doi.org/10.1016/j.fsigen.2022.102768
• The DNA Commission of the ISFG published recommendations regarding STR sequence nomenclature and the use of STRNaming:
  Gettings, K. B., Bodner, M., Borsuk, L. A., King, J. L., Ballard, D., Parson, W., Benschop, C. C. G., Børsting, C., Budowle, B., Butler, J. M., van der Gaag, K. J., Gill, P., Gusmão, L., Hares, D. R., Hoogenboom, J., Irwin, J., Prieto, L., Schneider, P. M., Vennemann, M., Phillips, C. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on short tandem repeat sequence nomenclature. Forensic Sci Int Genet, 68 (2023), 102946. doi.org/10.1016/j.fsigen.2023.102946
• The software is available from the Python Package Index (PyPI) at PyPI.org/project/FDSTools
• Bugs, feature requests and other issues can be reported and tracked at GitHub.com/Jerrythafast/FDSTools/issues
• Source code is available at GitHub.com/Jerrythafast/FDSTools