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Liu C, Wu P, Wu X, Zhao X, Chen F, Cheng X, Zhu H, Wang O, Xu M. AsmMix: an efficient haplotype-resolved hybrid de novo genome assembling pipeline. Front Genet 2024; 15:1421565. [PMID: 39130747 PMCID: PMC11310137 DOI: 10.3389/fgene.2024.1421565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Accurate haplotyping facilitates distinguishing allele-specific expression, identifying cis-regulatory elements, and characterizing genomic variations, which enables more precise investigations into the relationship between genotype and phenotype. Recent advances in third-generation single-molecule long read and synthetic co-barcoded read sequencing techniques have harnessed long-range information to simplify the assembly graph and improve assembly genomic sequence. However, it remains methodologically challenging to reconstruct the complete haplotypes due to high sequencing error rates of long reads and limited capturing efficiency of co-barcoded reads. We here present a pipeline, AsmMix, for generating both contiguous and accurate diploid genomes. It first assembles co-barcoded reads to generate accurate haplotype-resolved assemblies that may contain many gaps, while the long-read assembly is contiguous but susceptible to errors. Then two assembly sets are integrated into haplotype-resolved assemblies with reduced misassembles. Through extensive evaluation on multiple synthetic datasets, AsmMix consistently demonstrates high precision and recall rates for haplotyping across diverse sequencing platforms, coverage depths, read lengths, and read accuracies, significantly outperforming other existing tools in the field. Furthermore, we validate the effectiveness of our pipeline using a human whole genome dataset (HG002), and produce highly contiguous, accurate, and haplotype-resolved assemblies. These assemblies are evaluated using the GIAB benchmarks, confirming the accuracy of variant calling. Our results demonstrate that AsmMix offers a straightforward yet highly efficient approach that effectively leverages both long reads and co-barcoded reads for haplotype-resolved assembly.
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Affiliation(s)
- Chao Liu
- BGI, Tianjin, China
- BGI Research, Shenzhen, China
| | - Pei Wu
- BGI, Tianjin, China
- BGI Research, Shenzhen, China
| | - Xue Wu
- BGI Research, Shenzhen, China
| | | | | | | | - Hongmei Zhu
- BGI, Tianjin, China
- BGI Research, Shenzhen, China
| | - Ou Wang
- BGI Research, Shenzhen, China
| | - Mengyang Xu
- BGI Research, Shenzhen, China
- BGI Research, Qingdao, China
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Zhang Z, Xiao J, Wang H, Yang C, Huang Y, Yue Z, Chen Y, Han L, Yin K, Lyu A, Fang X, Zhang L. Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity. Nat Commun 2024; 15:4631. [PMID: 38821971 PMCID: PMC11143213 DOI: 10.1038/s41467-024-49060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 05/17/2024] [Indexed: 06/02/2024] Open
Abstract
Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range connectivity. Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads. Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and abundances, thereby improving the assembly of high- and medium-abundance microbial genomes. Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes. We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes. Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.
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Grants
- This research was partially supported by the Young Collaborative Research Grant (C2004-23Y, L.Z.), HMRF (11221026, L.Z.), the open project of BGI-Shenzhen, Shenzhen 518000, China (BGIRSZ20220012, L.Z.), the Hong Kong Research Grant Council Early Career Scheme (HKBU 22201419, L.Z.), HKBU Start-up Grant Tier 2 (RC-SGT2/19-20/SCI/007, L.Z.), HKBU IRCMS (No. IRCMS/19-20/D02, L.Z.).
- This research was partially supported by the open project of BGI-Shenzhen, Shenzhen 518000, China (BGIRSZ20220014, KJ.Y.).
- The study were partially supported by the Science Technology and Innovation Committee of Shenzhen Municipality, China (SGDX20190919142801722, XD.F.),
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Affiliation(s)
- Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Jin Xiao
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Hongbo Wang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | | | - Zhen Yue
- BGI Research, Sanya, 572025, China
| | - Yang Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, China
| | - Lijuan Han
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd (KMHD), Shenzhen, China
| | - Kejing Yin
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Xiaodong Fang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Sanya, 572025, China
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd (KMHD), Shenzhen, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China.
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Li D, Yu Q, Wu R, Tuo Z, Zhu W, Wang J, Shao F, Ye L, Ye X, Yoo KH, Ke M, Yang Y, Wei W, Feng D. Chronobiology of the Tumor Microenvironment: Implications for Therapeutic Strategies and Circadian-Based Interventions. Aging Dis 2024:AD.2024.0327. [PMID: 38607733 DOI: 10.14336/ad.2024.0327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Numerous research works have emphasized the critical role that circadian rhythm plays in the tumor microenvironment (TME). The goal of clarifying chrono-pharmacological strategies for improving cancer treatment in clinical settings is a continuous endeavor. Consequently, to enhance the use of time-based pharmaceutical therapies in oncology, combining existing knowledge on circadian rhythms' roles within the TME is essential. This perspective elucidates the functions of circadian rhythms in the TME across various stages of cancer development, progression, and metastasis. Specifically, aging, angiogenesis, and inflammation are implicated in modulating circadian rhythm within the TME. Furthermore, circadian rhythm exerts a profound influence on current cancer treatments and thereby generates chronotheray to manage tumors. From a TME perspective, circadian rhythm offers promising opportunities for cancer prevention and treatment; nevertheless, further study is needed to address unanswered scientific problems.
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Affiliation(s)
- Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Qingxin Yu
- Department of pathology, Ningbo Clinical Pathology Diagnosis Center, Ningbo, Zhejiang, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhouting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Weizhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Fanglin Shao
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Luxia Ye
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Xing Ye
- Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Koo Han Yoo
- Department of Urology, Kyung Hee University, Korea
| | - Mang Ke
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China
| | - Yubo Yang
- Department of Urology, Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
- Division of Surgery & Interventional Science, University College London, London W1W 7TS, UK
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Correction to "MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads". IMETA 2023; 2:e150. [PMID: 38868230 PMCID: PMC10989992 DOI: 10.1002/imt2.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
[This corrects the article DOI: 10.1002/imt2.46.].
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