GCI
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yeeus
A program for assessing the T2T genome continuity
hallo thank you for the gci and i am trying to use this for implementing in an analysis and it is giving this error. ``` Used arguments:{'reference': 'maternalpaternal.asm.dip.hap1.p_ctg.fa', 'hifi': ['ERR10930363.hifi.hap1.bam',...
Hi, when I extract only one chromosome of bam and fasta files to run, GCI stills outputs all chromosomes. The other chromosomes are null but the desired chromosome also failed....
Hi, Quanyu! thanks for your efforts to improve this nice tool. I am evaluating the assembly quality of centromeres and GCI can generate the score of a specific region. how...
Hi, It's a great tool! but i don't know how to input my depth file when used the plot_depth.py,can you give me an example? I also suggest that you cam...
Cool tool! I’m interested in specific regions, but I’m running into some issues with GCI. 1. Is it possible to generate a continuity index for a specific region? 2. When...
Dear yeeus, I think this is an excellent tool to map the depth and gaps of an assembly, but it does not succeed for me. It keeps killing the command...
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. 
Hi I would like to ask how to interpret outputs I want to confirm whether my MAGs are complete or circular GCI seems to be an index to evaluate the...
Hi developers, Thank you for this clean, powerful tool. Would this tool be applicable to primary assemblies?
