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yeeus / GCI

A program for assessing the T2T genome continuity
MIT License
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Curated contigs number can be zero ,even less than 1 #10

Open Frankie-zju opened 3 months ago

Frankie-zju commented 3 months ago

The final GCI-score result shows me that the curated contigs number can be zero, which will make the GCI-score infinity according to the formula. image

yeeus commented 3 months ago

Curated contigs number is computed by removing curated gaps on the contig so in few cases, the quality of the assembly is so poor, for example, that the contig might absolutely be "removed" and get the Curated contigs number zero. Other users had reported this issue and I had edited the code to make GCI score zero instead of infinity (which will get an error in python in reality). So this is normal for GCI and you maybe need to check your assembly or alignment files.