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Releases: linyuiz/CPhasing-mod

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Version 0.2

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@linyuiz linyuiz released this 31 Aug 01:49
v0.2
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Learn about vigilant mode.

1️⃣ Add mm2plus to replace minimap2.
2️⃣ Support Hi-C scaffolding and Pore-C scaffolding simultaneously.

❌ Don't download Source code.zip(tar.gz) !!!
⭐️ Download【zgtools】latest: https://github.com/linyuiz/zgtools/releases/

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Version 0.1

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@linyuiz linyuiz released this 24 Aug 05:06
v0.1
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Learn about vigilant mode.

Info

CPhasing-mod is a modified version of C-Phasing, featuring the following enhancements:
1️⃣ Refactor the nextflow + shell pipeline to improve script readability and maintainability.

2️⃣ Support simultaneous Hi-C/Pore-C clustering analysis across multiple data types, including but not limited to:
minibwa, bwa-mem2, _chromap, chromap, pairs.gz, and bam formats. The pipeline should generate multiple outputs such as .agp, .hic, and .assembly files accordingly.

3️⃣ Enable cross-compatibility among multiple .assembly files — they can share the same .hic file, while different .hic files differ only in interaction signal intensity, not in the underlying assembly structure.

4️⃣ Support both local execution and slurm cluster deployment, ensuring seamless job scheduling and resource management across environments.

5️⃣ Provide enhanced resumption capabilities for convenient continuation of interrupted runs, minimizing redundant computation and facilitating incremental updates.

❌ Don't download Source code.zip(tar.gz) !!!
⭐️ Download【zgtools】latest: https://github.com/linyuiz/zgtools/releases/

Citation

If you use CPhasing-mod in your work, please cite:

  • C-Phasing

    Yibin Wang, Ping Zhao, Xiaofei Zeng, Jiaxin Yu, Aoqian Dong, Yi Liu, Mengwei Jiang, Fang Wang, Xiao Chen, Shengcheng Zhang, Shuai Chen, Yuqing Gong, Yixing Zhang, Ruicai Long, Maojun Wang, Haibao Tang and Xingtan Zhang. Enhanced Pore-C with C-Phasing Enables Chromosomal-Scale, Haplotype-Resolved Assembly of Ultra-Complex Genomes, 05 November 2025, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-7343323/v1]

  • And HapHiC:

    Xiaofei Zeng, Zili Yi, Xingtan Zhang, Yuhui Du, Yu Li, Zhiqing Zhou, Sijie Chen, Huijie Zhao, Sai Yang, Yibin Wang, Guoan Chen. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. Nature Plants, 10:1184-1200. doi: https://doi.org/10.1038/s41477-024-01755-3

  • And ALLHiC

    Xingtan Zhang, Shengcheng Zhang, Qian Zhao, Ray Ming, Haibao Tang. (2019) Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nature Plants, 5:833-845. doi: https://doi.org/10.1038/s41477-019-0487-8

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