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dudcha authored Mar 16, 2021
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This version of the pipeline (201008) adds a JBAT-compatible phasing module to the pipeline.

For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see [Genome Assembly Cookbook](http://aidenlab.org/assembly/manual_180322.pdf) on http://aidenlab.org/assembly.
For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see [Genome Assembly Cookbook](http://aidenlab.org/assembly/manual_180322.pdf) on https://www.dnazoo.org/methods.

For the original version of the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in [(Dudchenko et al., *Science*, 2017)](http://science.sciencemag.org/content/356/6333/92) see the [original commit](https://github.com/theaidenlab/3d-dna/tree/745779bdf64db6e55bddb70c24e9b58825938c33).

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