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xingjianleng / DBGA

The repository for the genome sequence alignment research project
BSD 3-Clause "New" or "Revised" License
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evaluating alignment quality #22

Open GavinHuttley opened 1 year ago

GavinHuttley commented 1 year ago

where in dbga is the code for quantifying the alignment quality? (The squared-differences measure?)

xingjianleng commented 1 year ago

In the report the alignment_quality score from cogent3 was used for quantifying the alignment quality.

There is the implementation of the sum of pairs measure especially for multiple sequence alignment. The related paper is https://doi.org/10.1093/nar/27.13.2682 and the implementation is at https://github.com/xingjianleng/DBGA/blob/0da8dca853a98168dd858ad826b126827ee322b9/src/dbga/utils.py#L440-L534

GavinHuttley commented 1 year ago

move this statistic into cogent3 and making it an option via the Alignmentalignment_quality() method.