Journal
GIGASCIENCE
Volume 9, Issue 9, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giaa094
Keywords
gap closure; third-generation sequencing; genome assembly; ginkgo; MHC
Categories
Funding
- Shenzhen Municipal Government of China Peacock Plan [KQTD2015033017150531]
- National Key Research and Development Program of China [2018YFD0900301-05]
- Qingdao Applied Basic Research Projects [19-6-2-33-cg]
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Background: Analyses that use genome assemblies are critically affected by the contiguity, completeness, and accuracy of those assemblies. In recent years single-molecule sequencing techniques generating long-read information have become available and enabled substantial improvement in contig length and genome completeness, especially for large genomes (>100 Mb), although bioinformatic tools for these applications are still limited. Findings: We developed a software tool to close sequence gaps in genome assemblies, TGS-GapCloser, that uses low-depth (similar to 10x) long single-molecule reads. The algorithm extracts reads that bridge gap regions between 2 contigs within a scaffold, error corrects only the candidate reads, and assigns the best sequence data to each gap. As a demonstration, we used TGS-GapCloser to improve the scaftig NG50 value of 3 human genome assemblies by 24-fold on average with only similar to 10x coverage of Oxford Nanopore or Pacific Biosciences reads, covering with sequence data up to 94.8% gaps with 97.7% positive predictive value. These improved assemblies achieve 99.998% (Q46) single-base accuracy with final inserted sequences having 99.97% (Q35) accuracy, despite the high raw error rate of single-molecule reads, enabling high-quality downstream analyses, including up to a 31-fold increase in the scaftig NGA50 and up to 13.1% more complete BUSCO genes. Additionally, we show that even in ultra-large genome assemblies, such as the ginkgo (similar to 12 Gb), TGS-GapCloser can cover 71.6% of gaps with sequence data. Conclusions: TGS-GapCloser can close gaps in large genome assemblies using raw long reads quickly and cost-effectively. The final assemblies generated by TGS-GapCloser have improved contiguity and completeness while maintaining high accuracy. The software is available at https://github.com/BGI-Qingdao/TGS-GapCloser.
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