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Genome sequence assembly algorithms and misassembly identification methods

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Abstract

The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly mainly uses the iterative expansion of overlap relationships between sequences to construct the target genome. The assembly algorithms can be typically classified into several categories, such as the Greedy strategy, Overlap-Layout-Consensus (OLC) strategy, and de Bruijn graph (DBG) strategy. In particular, due to the rapid development of third-generation sequencing (TGS) technology, some prevalent assembly algorithms have been proposed to generate high-quality chromosome-level assemblies. However, due to the genome complexity, the length of short reads, and the high error rate of long reads, contigs produced by assembly may contain misassemblies adversely affecting downstream data analysis. Therefore, several read-based and reference-based methods for misassembly identification have been developed to improve assembly quality. This work primarily reviewed the development of DNA sequencing technologies and summarized sequencing data simulation methods, sequencing error correction methods, various mainstream sequence assembly algorithms, and misassembly identification methods. A large amount of computation makes the sequence assembly problem more challenging, and therefore, it is necessary to develop more efficient and accurate assembly algorithms and alternative algorithms.

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Abbreviations

bp:

Base pair

CCS:

Circular Consensus Sequencing

CLR:

Continuous Long Reads

DBG:

De Bruijn graph

DDF:

Distance difference factor

FBG:

Fuzzy-Bruijn graph

FCD:

Fragment coverage distribution

FPR:

False-positive rate

GFA:

Graph fragment assembly

GPU:

Graphics processing unit

HiFi:

High fidelity

HTS:

High-throughput sequencing

kb:

Kilobase pair

Mb:

Megabase pair

OLC:

Overlap-Layout-Consensus

POA:

Partial order alignment

QVs:

Quality values

SMRT:

Single-Molecule Real-Time

SNP:

Single nucleotide polymorphism

SV:

Structural variation

SVs:

Structural variations

tf-idf :

Term frequency, inverse document frequency

TGS:

Third-generation sequencing

WGS:

Whole-genome sequencing

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Funding

This work was supported by grants from the National Natural Science Foundation of China (61902094), the Heilongjiang Provincial Natural Science Foundation of China (QC2018082), the Shandong Provincial Natural Science Foundation of China (ZR2021MH036), the Science and Technology Program of Binzhou Medical University (50012304325), the Fundamental Research Funds for the Central University (2017-KYYWF-0140), the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province (UNPYSCT) (UNPYSCT-2018183), the Doctoral Scientific Research Foundation of Harbin Normal University (XKB201916, XKB201801), the Science Foundation of School of Computer Science and Information Engineering of Harbin Normal University (JKYKYZ202004, JKYKYZ202104), and the Graduate Innovative Research Project of Harbin Normal University (HSDSSCX2021-31).

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  1. Yue Meng, Yu Lei and Jianlong Gao have contributed equally to this work.

Authors and Affiliations

  1. School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China

    Xiao Zhu

  2. School of Information Engineering, Zhengzhou University of Industrial Technology, Zhengzhou, Henan, China

    Yue Meng

  3. School of Computer Science and Information Engineering, Harbin Normal University, Harbin, Heilongjiang, China

    Jianlong Gao, Yuxuan Liu, Enze Ma, Yunhong Ding & Yixin Bian

  4. Department of Big Data and Intelligent Engineering, Shanxi Institute of Technology, Yangquan, Shanxi, China

    Yu Lei

  5. Center of Network and Information, Harbin Institute of Technology, Harbin, Heilongjiang, China

    Hongquan Zu

  6. Department of Immunology, Binzhou Medical University, Yantai, Shandong, China

    Yucui Dong

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  1. Yue Meng
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Contributions

YM, YL (Yu Lei) and JG conceptualized and wrote the manuscript. YL (Yuxuan Liu), EM and YD (Yunhong Ding) prepared the figures. YB and HZ prepared the tables. YD (Yucui Dong) and XZ revised this review. All authors read and approved the final manuscript.

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Correspondence to Yucui Dong or Xiao Zhu.

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Meng, Y., Lei, Y., Gao, J. et al. Genome sequence assembly algorithms and misassembly identification methods. Mol Biol Rep 49, 11133–11148 (2022). https://doi.org/10.1007/s11033-022-07919-8

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