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Computational methods for chromosome-scale haplotype reconstruction
Open accessAbstract
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.
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“Pstools reported slightly lower switch error rates than Yak but comparable Hamming error rates (Supplementary Fig. 2).”
From A draft human pangenome reference. (2023) · cites this paper as [23]
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Cited by
Sorted by citations
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Raza, A., Zaman, Q. U., Shabala, S. N., Tester, M. A., Munns, R., Hu, Z., & Varshney, R. K. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70104 · Cited by 66
“…and superior GS models will significantly aid in fast-tracking the supply of superior breeding lines with SST. Haplotypes, combinations of alleles inherited together on similar Chr, play a critical role in plant breeding for designing advanced crop varieties (Bhat et al ., 2021; Garg, 2021).”
InfluentialGenomic and modern biotechnological strategies for enhancing salt tolerance in crops
Yuan, J., Cao, H., Qin, W., Yang, S., Zhang, D., Zhu, L., Song, H., & Zhang, Q. (2024) · New Crops · doi:10.1016/j.ncrops.2024.100057 · Cited by 60
A Draft Human Pangenome ReferencePreprint
Liao, W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J., Monlong, J., Abel, H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.09.499321 · Cited by 58
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Self-citationGenomics-assisted speed breeding for crop improvement: present and future
Ćeran, M., Miladinović, D., Đorđević, V., Trkulja, D., Radanović, A., Glogovac, S., & Kondić‐Špika, A. (2024) · Frontiers in Sustainable Food Systems · doi:10.3389/fsufs.2024.1383302 · Cited by 54
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“These alleles of various polymorphisms existing on a segment of chromosome are inherited together with a minimum chance of contemporary recombination (Garg 2021; Sehgal et al.”
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Luo, X., Kang, X., & Schönhuth, A. (2022) · Genome biology · doi:10.1186/s13059-021-02587-6 · Cited by 36
Complex genome assembly based on long-read sequencing
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Sequencing and Assembly of Polyploid Genomes
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“For highly heterozygous diploid and polyploid organisms, a haplotype-phased genome represents the ultimate goal of dissecting genomes and allows breeders to capture the effect of allelic gene function [8].”
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“In this section, we present the comprehensive and detailed methodology for the analysis of metagenomic raw data 64 , addressing every aspect from initial quality control to the fi nal annotation and classi fi - cation stages/MAG production: 1.”
Self-citationThe importance of fungal biotechnology for sustainable applications
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Self-citationChromosome-scale haplotype-resolved pangenomics
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“On the other hand more and more approaches desire phased assemblies, where both homologous chromosome sets are part of the assembly [192, 193].”
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TopoQual polishes circular consensus sequencing data and accurately predicts quality scores
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Can long-read sequencing tackle the barriers, which the next-generation could not? A review
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“Haplotypes within a diploid chromosome are determined by fi nding a partitioning of reads to two sets, one for each haplotype, such that the reads within subsets have a minimal number of errors compared to a consensus [106].”
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“This is mainly due to the limitation of NGS itself in identifying repetitive sequences, etc., which affects the fi nal haplotype resolution (Mantere et al., 2019; Garg, 2021).”
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Geometric deep learning framework for de novo genome assemblyPreprint
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“As suggested by (35), we considered ConStrains (36), StrainFinder (37), Gretel (38) and DESMAN (28) as currently leading tools.”
BackgroundMethodEditorial: Long-read sequencing—Pitfalls, benefits and success stories
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“Already, long-read sequencing can be used to reach an unprecedented genetic resolution (Garg, 2021), e.g. by covering previously inaccessible genomic regions or entire RNA transcripts in individual reads.”
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A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms
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“Phase can be estimated with computational methods that rely on haplotype evidence from multiple sources; different software programs may support one or more of the following sources: haplotype reference panel, sequence reads, and/or familial genotypes [1, 5–7].”
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“One future direction of work would be to adapt the model for diploid features 34 .”
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“Complete sequence information of eccDNA will be obtained by long-read sequencing, and structural variation can be observed to analyze the differential functions of eccDNA (Garg, 2021).”
Targeted sequencing and iterative assembly of near-complete genomes
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“The capacity to obtain high quality and even complete telomere-to-telomere (T2T) assemblies for large eukaryotic genomes is transforming our understanding of genome architecture, variation and evolution 1 – 3 .”
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“…scale haplotype ‐ resolved assemblies, the inter - actions between variants in regulator elements can be more clearly understood (Tewhey et al., 2011) as well as the interplay of the evolutionary processes that a ff ect genetic variation, such as recombination, mutation, and selection (Garg, 2021).”
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GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs
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KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost
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“One tool, known asWHdenovo, can apply pedigree information and long-sequence reads to enhance the construction of sample-specific assemblies that can resolve potential genotyping errors in this workflow (Garg et al. 2020; Garg 2021).”
MethodNavarro, A. T., Bourke, P. M., Weg, E. W. V. D., Clot, C. R., Arens, P. F. P., Finkers, R., & Maliepaard, C. A. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1049988 · Cited by 5
“Multiple tools have been developed to produce long-range haplotypes using short reads, long reads or a combination of both (Garg, 2021).”
BackgroundMethodAutomated filtering of genome-wide large deletions through an ensemble deep learning framework
Hu, Y., Mangal, S., Zhang, L., & Zhou, X. (2022) · Methods · doi:10.1016/j.ymeth.2022.08.001 · Cited by 4
The Telomere-Telomerase System Is Detrimental to Health at High-Altitude
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SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs
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“For large genomes and metagenomes, long high-fi delity (HiFi) reads proved to be useful in generating highly-accurate and contiguous assemblies ( Nurk et al., 2020 ; Sha fi n et al., 2020 ; Kolmogorov et al., 2020 ; Cheng et al., 2021 ; Nurk et al., 2022 ; Rautiainen et al., 2023 ; Garg, 2021 ).”
BackgroundZeng, Q., Cao, W., Li, W. L., Wu, J., Figueroa, M., Liu, H., Qin, G., Wang, Q., Yang, L., Zhou, Y., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.18.484966 · Cited by 4
Genomics-Assisted Breeding for Fodder Quality Improvement in Forage Sorghum
Behera, P. P., & Sarma, R. N. (2025) · Springer eBooks · doi:10.1007/978-3-032-04527-0_3 · Cited by 3
Du, H., Lun, M. Y., Gagarina, L., Bengtsson, J. D., Grochowski, C. M., Mehaffey, M. G., Hwang, J. P., Jhangiani, S. N., Bhamidipati, S. V., Muzny, D. M., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01593-8 · Cited by 3
“…read depth, B-allele frequency (BAF) information, and haplotype phasing to the CNV analysis has been pivotal in high-impact variant prioritization [3, 4], and enables the identification of: i) de novo CNVs – i.e. mutations present only in the proband, but not in either parent [5], ii) homozygous…”
Pan-genomics of polyploid crops: from complexity to breeding
Naik, Y. D., Thudi, M., Kamal, N. M., Egan, A. N., Janga, M. R., & Puppala, N. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1800432 · Cited by 4
“The computational requirements also increase substantially with higher ploidy levels, as the number of possible haplotypes grows exponentially (Garg, 2021).”
Characteristics and potential functional effects of long insertions in Asian butternuts
Chen, Y., Miao, Y., Bai, W., Lin, K., & Pang, E. (2022) · BMC Genomics · doi:10.1186/s12864-022-08961-3 · Cited by 3
“representation is one major challenge [9] though there are methods such as chromosome-scale haplotype reconstruction [14] to account for this.”
MethodStatistical and Computational Methods for Microbial Strain Analysis
Ma, S., & Li, H. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2986-4_11 · Cited by 2
BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies
Höjer, P., Frick, T., Siga, H., Pourbozorgi, P. L., Aghelpasand, H., Martin, M., & Ahmadian, A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1010 · Cited by 3
“Repetitive regions remain a challenge for accurate phasing ( 7 ).”
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points
Zhang, W., Tariq, A., Jia, X., Yan, J., Fernie, A. R., Usadel, B., & Wen, W. (2024) · Nature Protocols · doi:10.1038/s41596-024-01063-2 · Cited by 3
Jeon, H., Bae, J., Kim, H., & Kim, M. (2021) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2021.3138145 · Cited by 3
Revisiting the Genomic Approaches in the Cereals and the Path Forward
Kaur, I., Relan, A., Saini, D. K., Kaur, G., Biswas, A., Singh, L., Kaur, S., & Sandhu, K. S. (2023) · Springer eBooks · doi:10.1007/978-981-19-8218-7_1 · Cited by 3
Haplotype-Assisted Breeding in Rice
Sagar, U. S. S. V., Pushpam, R., Raveendran, M., Kulkarni, V., & Rajanna, B. (2024) · Springer eBooks · doi:10.1007/978-981-97-7098-4_7 · Cited by 3
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences
Fruzangohar, M., Timmins, W. A., Kravchuk, O. Y., & Taylor, J. (2022) · GigaScience · doi:10.1093/gigascience/giac038 · Cited by 3
“For example, the algorithm could be used to assemble haplotypes for genomes from tetraploid and hexaploid species, such as wheat, as long as there are separate reference sequences for each of the homoeologous copies of the chromosomes [1].”
InfluentialFilling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
Huang, B., Wei, G., Wang, B., Ju, F., Zhong, Y., Shi, Z., Sun, S., & Bu, D. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04448-2 · Cited by 3
“The study [6] provides an elaborated review on the methodological progresses and perspectives in the integration of short-range and long-range information for improving assembly contiguity.”
BackgroundKumari, J., Kumari, V., Thakur, R., Kapoor, R., Priyanka, Kumari, S., & Chaturvedi, V. D. (2025) · Australian Journal of Agricultural Research · doi:10.1071/cp24139 · Cited by 2
Muduli, B. C., Selvaraj, S., Sahu, S., Dhall, S., Swain, N., Parameswaran, C., Meher, J., Pradhan, C., Chatterjee, D., Mohanty, S., et al. (2025) · 3 Biotech · doi:10.1007/s13205-025-04350-1 · Cited by 2
“A haplotype is a combination of alleles for different polymorphisms (such as SNPs, insertions/deletions and other markers or variants) on the same chromosome and region, inherited with minimal chance of recombination (Stram et al. 2017; Garg et al. 2021).”
Navarro, A. T., Bourke, P. M., Weg, E. W. V. D., Arens, P. F. P., Finkers, R., & Maliepaard, C. A. (2022) · Research Square · doi:10.21203/rs.3.rs-1165750/v1 · Cited by 2
Review on Advancement of AI in Cell Engineering and Molecular Biology
Swargiary, D., Saikia, A., Basumatary, D., & Borah, J. C. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4690-8_10 · Cited by 1
Exploring standing genetic variation for barley leaf rust resistance in Australian breeding panel
Pandit, M., Dracatos, P. M., Periyannan, S. K., Lam, Y., Brunner, S. M., Honse, T., Tong, J., Dinglasan, E. G., Ganesalingam, A., Moody, D. B., et al. (2026) · Theoretical and Applied Genetics · doi:10.1007/s00122-025-05122-4 · Cited by 1
“A haplotype-based association mapping has proven effective for identifying genomic loci and candidate genes underlying quantitative traits (Abed and Belzile 2019; Hamazaki and Iwata 2020; Garg 2021; Bhat et al. 2021).”
Trait Discovery in the Post-NGS Era
Rathore, M., Jan, F., Aggarwal, N., Bashir, M., Prasad, S. H., Khan, M. A., Sofi, P. A., Chitikineni, A., Saini, D. K., & Mir, R. R. (2026) · Sustainability Sciences in Asia and Africa · doi:10.1007/978-981-95-5109-5_12 · Cited by 1
HAT: haplotype assembly tool using short and error-prone long reads
Zade, R. S. H., Urhan, A., de Souza, A. A., Singh, A., & Abeel, T. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac702 · Cited by 1
“On the other hand, in polyploid genomes, other haplotypes may have the same or different alleles (Garg, 2021).”
BackgroundGCphase: an SNP phasing method using a graph partition and error correction algorithm
Luo, J., Wang, J., Zhai, H., & Wang, J. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05901-8 · Cited by 1
Jeline Rani, J., & Nandagopalan, V. (2023) · International Journal of Pharmaceutical Sciences and Drug Research · doi:10.25004/ijpsdr.2023.150319 · Cited by 1
Navarro, A. T. (2023) · doi:10.18174/630278 · Cited by 1
Navarro, A. T., Bourke, P. M., Weg, E. W. V. D., Clot, C. R., Arens, P. F. P., Finkers, R., & Maliepaard, C. A. (2022) · Research Square · doi:10.21203/rs.3.rs-1165750/v2
Pairwise comparative analysis of six haplotype assembly methods based on users’ experience
Sun, S., Cheng, F., Han, D., Wei, S., Zhong, A., Massoudian, S., & Johnson, A. B. (2023) · BMC Genomic Data · doi:10.1186/s12863-023-01134-5
“However, there remain different challenges in haplotype assembly for repetitive regions, in scaling haplotype reconstruction efforts for routine applications, in validation, in benchmarking, and in annotation [7].”
BackgroundAsmMix: an efficient haplotype-resolved hybrid de novo genome assembling pipeline
Liu, C., Wu, P., Wu, X., Zhao, X., Chen, F., Cheng, X., Zhu, H., Wang, O., & Xu, M. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1421565
“Hi-C data provides information about the spatial organization of the genome, allowing for the analysis of long-range haplotyping and scaffolding at the chromosome level (Garg et al., 2021).”
BackgroundMethodInfluentialGong, T., Zhou, Y., Huang, Y., Zhao, J., Gong, J., Li, J., Peng, Q., Wang, S., Li, J., & Fan, S. (2024) · Research Square · doi:10.21203/rs.3.rs-5343403/v1
Fan, S., Gong, T., Zhou, Y., Zhao, J., Huang, Y., Gong, J., Li, J., Peng, Q., Chang, H., Yuan, L., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-6312842/v1
Genomics-Assisted Breeding: A Revolutionary Approach for Sugarcane Development
Naik, Y. D., Keshari, A. K., Kurhade, A. K., Patil, V. S., Veerendrakumar, H. V., Jadhav, M. P., & Upadhayay, V. K. (2025) · Springer eBooks · doi:10.1007/978-981-96-6871-7_15
Methods for Chromosome-Scale Haplotype Reconstruction
Garg, S. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4702-8_2
Self-citationDirect inference of haplotypes from sequencing data
Zhang, Z., Zhu, B., Luo, Y., Shi, J., Lian, S., Hao, J., Hu, T., Ishibashi, T., Wang, D., Wang, S., et al. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf195
“But more than two haplotypes may exist at any given chromosomal region when genotyping polyploid genomes or a mixture of diploid cell populations, which is common for sequencing tumor tissues contaminated with normal cells (Garg 2021).”
Local Haplotyping Analysis for Flowering Time in Soybean Using Crosshap
Mohamedikbal, S., Upadhyaya, S. R., Bestry, M., Marsh, J. I., & Edwards, D. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4820-9_6
Chen, S., Lee, E.-G., Leong, L., Tulloch, J., & Yu, C. (2025) · Research Square · doi:10.21203/rs.3.rs-7634101/v1
Metadata
- Authors
- Garg, S.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Garg, Shilpa
- ORCID
- Garg, Shilpa
- Venue
- Genome Biology
- Published
- 2021-04-12
- Volume
- 22
- Issue
- 1
- Pages
- 101-101
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC8040228
- OpenAlex
- W3156261638
- Cited by
- 116
- References
- 154
- Citations by year
- 2026: 11 · 2025: 26 · 2024: 25 · 2023: 20 · 2022: 28 · 2021: 6
- FWCI
- 2.07
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- haplotype reconstruction, haplotype assembly, diploid genome, polyploid genomes, metagenome, long-read sequencing, repetitive regions, genetic variation
- MeSH terms
- Chromosomes, Diploidy, Haplotypes, Humans, Polyploidy, Sequence Analysis, DNA, Computational Biology, Genomics, Metagenome, Metagenomics, High-Throughput Nucleotide Sequencing
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