MetaCONNET: A metagenomic polishing tool for long-read assemblies
Accurate and high coverage genome assemblies are the basis for downstream analysis of metagenomic studies. Long-read sequencing technology is an ideal tool to facilitate the assemblies of metagenome, except for the drawback of usually producing reads with high sequencing error rate. Many polishing tools were developed to correct the sequencing error, but most are designed on the ground of one or two species. Considering the complexity and uneven depth of metagenomic study, we present a novel deep-learning polishing tool named MetaCONNET for polishing metagenomic assemblies. We evaluate MetaCONNET against Medaka, CONNET and NextPolish in accuracy, coverage, contiguity and resource consumption. Our results demonstrate that MetaCONNET provides a valuable polishing tool and can be applied to many metagenomic studies.
Authors
- Jian Guo (ORCID: https://orcid.org/0000-0002-0314-4080)
- Zijie Jin (ORCID: https://orcid.org/0000-0002-0042-3295)
- Hao Jin (ORCID: https://orcid.org/0000-0003-2965-0739)
- Zhihong Sun (ORCID: https://orcid.org/0000-0002-7605-2048)
- Igor Ivanov
- Hui Tian (ORCID: https://orcid.org/0000-0002-4517-2776)
- Yun He (ORCID: https://orcid.org/0000-0002-5322-7300)
- Wei Li (ORCID: https://orcid.org/0000-0003-4475-531X)
- Yaping Sun
- Bingru Sun
- Yuanchen Mao
- Fuli Xie
Institutions
- Inner Mongolia Agricultural University (CN)
- Peking University (CN)
- Beike Biotechnology (China) (CN)
- Peking University International Hospital (CN)
Publication Details
- Journal
- PLoS ONE
- Published
- 2024-12-03
- DOI
- https://doi.org/10.1371/journal.pone.0313515
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Innovative Research Group Project of the National Natural Science Foundation of China
- National Natural Science Foundation of China
- China Postdoctoral Science Foundation