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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...P, Bafna V, Bansal V. 2017. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res 27: 801–812. doi:10.1101/gr.213462.116 ↵Gamaarachchi H, Samarakoon H, Jenner SP, Ferguson JM, Amos TG, Hammond JM, Saadat H, Smith MA, Parameswaran S, Deveson IW. 2022. Fast...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...with various long-read sequencing technologies. On a synthetic Oxford Nanopore Technologies (ONT) long-read data set containing seven HIV strains, devider recovers 97% of the haplotype content and has the most accurate abundance estimates while taking <4 min and 1 GB of memory for >8000× coverage. Benchmarking...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...-span haplotypes for use in assigning “omic” data from diploid s to their parental origins, we performed reciprocal crosses of two genetically distinct pig breeds (three families of Tibetan [♂] × Berkshire [♀], and three families of Berkshire [♂] × Tibetan [♀]) and sequenced the whole s of six parent–child trios...
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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...derived from existing SV annotations or clinically relevant loci. By combining the accuracy of assembly-based methods with the efficiency of region-specific processing, FocalSV delivers robust and scalable performance across diverse sequencing technologies and SV types. Together, these modes establish...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...to cytoplasmic RNA across samples (Supplemental Fig. S1B).To enable allele-specific analyses, we used the software LORALS (Glinos et al. 2022) to map nanopore sequencing reads to two personalized reference s per LCL and we determined their allele of origin using HapCUT2 (Supplemental Fig. S1C; Edge et al. 2017...
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Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
- Zhoutao Chen,
- Long Pham,
- Tsai-Chin Wu,
- Guoya Mo,
- Yu Xia,
- Peter L. Chang,
- Devin Porter,
- Tan Phan,
- Huu Che,
- Hao Tran,
- Vikas Bansal,
- Justin Shaffer,
- Pedro Belda-Ferre,
- Greg Humphrey,
- Rob Knight,
- Pavel Pevzner,
- Son Pham,
- Yong Wang,
- and Ming Lei
Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
...calls (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GRCh38/) using the Illumina haplotype VCF comparison tool, hap.py (https://github.com/Illumina/hap.py.git).Phasing linked-reads using HapCUT2Linked-reads were phased with HapCUT2 (https://github.com/vibansal/HapCUT2) using...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
...of a HapMap trio child: evaluation of Single Individual Haplotyping techniques. Nucleic Acids Res 40: 2041–2053. doi:10.1093/nar/gkr1042 ↵Edge P, Bafna V, Bansal V. 2017. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res 27: 801–812. doi:10.1101/gr.213462...
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Method: An efficient genotyper and star-allele caller for pharmacogenomics
- Ananth Hari,
- Qinghui Zhou,
- Nina Gonzaludo,
- John Harting,
- Stuart A. Scott,
- Xiang Qin,
- Steve Scherer,
- S. Cenk Sahinalp,
- and Ibrahim Numanagić
Genome Res. January 2023 33: 61-70; Published in Advance January 19, 2023, doi:10.1101/gr.277075.122
...: 572–587. doi:10.1038/s41576-021-00367-3 ↵Edge P, Bafna V, Bansal V. 2017. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res 27: 801...
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Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- Ryan Lorig-Roach,
- Melissa Meredith,
- Jean Monlong,
- Miten Jain,
- Hugh E. Olsen,
- Brandy McNulty,
- David Porubsky,
- Tessa G. Montague,
- Julian K. Lucas,
- Chris Condon,
- Jordan M. Eizenga,
- Sissel Juul,
- Sean K. McKenzie,
- Sara E. Simmonds,
- Jimin Park,
- Mobin Asri,
- Sergey Koren,
- Evan E. Eichler,
- Richard Axel,
- Bruce Martin,
- Paolo Carnevali,
- Karen H. Miga,
- and Benedict Paten
Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
...to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta assembler and a modular tool for extending phasing to the chromosome scale called...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...) and haplotypes (e.g., HP1, HP2).There are two main methods for phasing: WhatsHap (Martin et al. 2023) and HapCUT2 (Edge et al. 2017). Other SNV-based phasing methods include LongPhase (Lin et al. 2022a) and HiPhase (Holt et al. 2024), which can incorporate SVs. A novel method, MethPhaser, extends the SNV...

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