Accurate assembly of full-length consensus for viral quasispecies
Abstract Background Viruses can inhabit their hosts in the form of an ensemble of various mutant strains. Reconstructing a robust consensus representation for these diverse mutant strains is essential for recognizing the genetic variations among strains and delving into aspects like virulence, patho...
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BMC
2025-02-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06045-z |
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| author | Jia Tian Ziyu Gao Minghao Li Ergude Bao Jin Zhao |
| author_facet | Jia Tian Ziyu Gao Minghao Li Ergude Bao Jin Zhao |
| author_sort | Jia Tian |
| collection | DOAJ |
| description | Abstract Background Viruses can inhabit their hosts in the form of an ensemble of various mutant strains. Reconstructing a robust consensus representation for these diverse mutant strains is essential for recognizing the genetic variations among strains and delving into aspects like virulence, pathogenesis, and selecting therapies. Virus genomes are typically small, often composed of only a few thousand to several hundred thousand nucleotides. While constructing a high-quality consensus of virus strains might seem feasible, most current assemblers only generated fragmented contigs. It’s important to emphasize the significance of assembling a single full-length consensus contig, as it’s vital for identifying genetic diversity and estimating strain abundance accurately. Results In this paper, we developed FC-Virus, a de novo genome assembly strategy specifically targeting highly diverse viral populations. FC-Virus first identifies the k-mers that are common across most viral strains, and then uses these k-mers as a backbone to build a full-length consensus sequence covering the entire genome. We benchmark FC-Virus against state-of-the-art genome assemblers. Conclusion Experimental results confirm that FC-Virus can construct a single, accurate full-length consensus, whereas other assemblers only manage to produce fragmented contigs. FC-Virus is freely available at https://github.com/qdu-bioinfo/FC-Virus.git . |
| format | Article |
| id | doaj-art-384d2fc34fb14108a466197441c46e04 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
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| series | BMC Bioinformatics |
| spelling | doaj-art-384d2fc34fb14108a466197441c46e042025-02-02T12:45:01ZengBMCBMC Bioinformatics1471-21052025-02-0126111510.1186/s12859-025-06045-zAccurate assembly of full-length consensus for viral quasispeciesJia Tian0Ziyu Gao1Minghao Li2Ergude Bao3Jin Zhao4College of Computer Science and Technology, Qingdao UniversityCollege of Computer Science and Technology, Qingdao UniversityCollege of Computer Science and Technology, Qingdao UniversitySchool of Software Engineering, Beijing Jiaotong UniversityCollege of Computer Science and Technology, Qingdao UniversityAbstract Background Viruses can inhabit their hosts in the form of an ensemble of various mutant strains. Reconstructing a robust consensus representation for these diverse mutant strains is essential for recognizing the genetic variations among strains and delving into aspects like virulence, pathogenesis, and selecting therapies. Virus genomes are typically small, often composed of only a few thousand to several hundred thousand nucleotides. While constructing a high-quality consensus of virus strains might seem feasible, most current assemblers only generated fragmented contigs. It’s important to emphasize the significance of assembling a single full-length consensus contig, as it’s vital for identifying genetic diversity and estimating strain abundance accurately. Results In this paper, we developed FC-Virus, a de novo genome assembly strategy specifically targeting highly diverse viral populations. FC-Virus first identifies the k-mers that are common across most viral strains, and then uses these k-mers as a backbone to build a full-length consensus sequence covering the entire genome. We benchmark FC-Virus against state-of-the-art genome assemblers. Conclusion Experimental results confirm that FC-Virus can construct a single, accurate full-length consensus, whereas other assemblers only manage to produce fragmented contigs. FC-Virus is freely available at https://github.com/qdu-bioinfo/FC-Virus.git .https://doi.org/10.1186/s12859-025-06045-zViral genome assemblyConsensusHomologous k-mersVial quasispecies |
| spellingShingle | Jia Tian Ziyu Gao Minghao Li Ergude Bao Jin Zhao Accurate assembly of full-length consensus for viral quasispecies BMC Bioinformatics Viral genome assembly Consensus Homologous k-mers Vial quasispecies |
| title | Accurate assembly of full-length consensus for viral quasispecies |
| title_full | Accurate assembly of full-length consensus for viral quasispecies |
| title_fullStr | Accurate assembly of full-length consensus for viral quasispecies |
| title_full_unstemmed | Accurate assembly of full-length consensus for viral quasispecies |
| title_short | Accurate assembly of full-length consensus for viral quasispecies |
| title_sort | accurate assembly of full length consensus for viral quasispecies |
| topic | Viral genome assembly Consensus Homologous k-mers Vial quasispecies |
| url | https://doi.org/10.1186/s12859-025-06045-z |
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