David Lougheed
@davidlougheed.bsky.social
Bioinformatics software developer at the Canadian Centre for Computational Genomics, Montreal. https://dlougheed.com
STRkit still does support a degree of deviation from the reference motif, even with only the reference genome motif as input. (3/3)
April 1, 2025 at 1:12 PM
STRkit still does support a degree of deviation from the reference motif, even with only the reference genome motif as input. (3/3)
... or the poly-alanine expansion in HOXA13/HOXD13 which causes HFGS (doi:10.1007/s00439-002-0712-8), but it's not as flexible as TRGT's system for instance, which supports a pattern (see github.com/PacificBiosc...) (2/3)
April 1, 2025 at 1:12 PM
... or the poly-alanine expansion in HOXA13/HOXD13 which causes HFGS (doi:10.1007/s00439-002-0712-8), but it's not as flexible as TRGT's system for instance, which supports a pattern (see github.com/PacificBiosc...) (2/3)
Thanks for the question! It depends on the degree of deviation, and knowledge of the tandem repeat - the user can specify a motif with IUPAC codes in the input repeat catalog, which would work for something like the SCA37-causing DAB1 repeat ([RAAAG]n; doi:10.1016/j.ajhg.2017.06.007) (1/3)
April 1, 2025 at 1:12 PM
Thanks for the question! It depends on the degree of deviation, and knowledge of the tandem repeat - the user can specify a motif with IUPAC codes in the input repeat catalog, which would work for something like the SCA37-causing DAB1 repeat ([RAAAG]n; doi:10.1016/j.ajhg.2017.06.007) (1/3)
STRkit is available as a Python package, and the source code is available on GitHub: github.com/davidloughee...
GitHub - davidlougheed/strkit: A short tandem repeat (STR) genotyping and analysis toolkit for long reads
A short tandem repeat (STR) genotyping and analysis toolkit for long reads - davidlougheed/strkit
github.com
March 29, 2025 at 1:01 PM
STRkit is available as a Python package, and the source code is available on GitHub: github.com/davidloughee...