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mdozmorov / HiC_tools

A collection of tools for Hi-C data analysis
MIT License
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Some other hic scaffolder #8

Open xiekunwhy opened 2 years ago

xiekunwhy commented 2 years ago

Hi,

I found some other hic scaffolders https://github.com/dfguan/pin_hic https://github.com/kingforest93/EndHiC(https://github.com/fanagislab/EndHiC) https://github.com/wtsi-hpag/scaffHiC

Best, Kun

mdozmorov commented 2 years ago

Thanks, Kun. I wish they would be published, or at least have preprints. If you are familiar with any, please, write a summary and make a PR.

xiekunwhy commented 2 years ago

Thank you for your reply, I am not so familiar whith them, and I am now trying them, I will make a PR if some of them have a good performance.

xiekunwhy commented 2 years ago

Hi,

The paper of pin_hic and endhic have been published. pin_hic: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04453-5 endhic(preprint): https://arxiv.org/abs/2111.15411

endhic has a better performance than others if N90 is longer enough, in my opinion.

Best, Kun

mdozmorov commented 2 years ago

Thanks, Kun. Both are on my reading list