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treangenlab / Olivar

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
https://doi.org/10.1038/s41467-024-49957-9
GNU General Public License v3.0
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Optimization for short input genome #2

Closed mxwang66 closed 7 months ago

mxwang66 commented 11 months ago

When input genome is short compared to desired amplicon length (e.g., less than 20 amplicons to cover the whole genome), optimize for genome coverage. Loss should be multiplied by 1/coverage.

mxwang66 commented 7 months ago

see v1.1.4 Updated Loss function for short genomes (Loss is multiplied by 1/coverage^2).