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Oshlack / STRetch

Method for detecting STR expansions from short-read sequencing data
MIT License
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difference between stretch and strling? #66

Closed hchetia closed 3 years ago

hchetia commented 3 years ago

Could you elaborate on the differences between STRetch and STRling?

hdashnow commented 3 years ago

The key conceptual differences are that STRetch requires an STR genome annotation (provided), so that it can only call known loci. In contrast STRling (https://github.com/quinlan-lab/STRling) infers the location off STR loci from the reads, so can find both known and novel STR loci (e.g. pathogenic STR loci or alleles are absent from the reference genome: CANVAS, Baratela-Scott Syndrome, and several forms of FAME epilepsy and SCA). Algorithmically, STRling is also faster because it doesn't remap reads. STRetch may be more sensitive for some known loci.

hchetia commented 3 years ago

Thanks.