Claim · model-written summary
The authors suggest using high-precision CCS reads to polish the assembly to correct errors effectively for polyploid genomes.
- Taxon
- Veratrum dahuricum
Veratrum dahuricume0 - Outcome
- polish the assembly to correct those errorse1
Not reportedMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleTreatmentComparatorSettingDirectionValueQualifier
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Veratrum dahuricum”
e1“We suggest high-precision CCS reads be used to polish the assembly to correct those errors effectively for polyploid genomes”
Title
Peng Zeng; Zunzhe Tian; Yuwei Han; et al. Chinese Medicine 2022. doi:10.1186/s13020-022-00644-1
Other claims from this paper (8)
- Method / resource The coverage of the three ONT assemblies of Veratrum dahuricum by NGS reads ranged from 49.15 to 76.31%, much smaller than that of the CCS assembly.
- Method / resource The CCS assembly of Veratrum dahuricum was covered by NGS reads at 99.53%, far above the ONT assemblies.
- Method / resource Alignment between ONT assemblies and the CCS assembly showed that most uncovered regions (UCR) could be aligned with the CCS assembly.
- Observation The uncovered regions in the ONT assembly are low-quality sequences with a high error rate that cannot be aligned with short reads, not unsequenceable genomic regions.
- Mechanism The most probable origin of errors in the ONT assemblies is a combination of artificial errors introduced by self-correction and initial sequencing error in long reads.
- Intervention effect Polishing the ONT assembly with CCS reads corrected the errors efficiently.
- Intervention effect Self-correction of ONT reads introduces artificial errors into more than 5% of the UCR sequences.
- Observation A considerable proportion of published allotetraploid long-read genomes (7.9% on average, maximum 23.7%) could not be covered by NGS reads.