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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
...contig were assessed using CheckM (Parks et al. 2015), using marker genes that are specific to each species inferred lineage within a reference tree. Second, CheckM and the Genome Taxonomy Database Toolkit (GTDB-Tk) (Chaumeil et al. 2020, 2022) were used to identify and classify the assembled bacterial...
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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...of SCGs is selected based on their presence in all bacterial s, or at least all s within a taxonomic group (identified based on the phylogeny). In a without contamination, they should be present without redundancy. A widely used tool to assay both completeness and contamination is CheckM (Parks et al...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...studies using short reads alone struggle to assemble complete s; however, the emergence of complete metagenomics (Bickhart et al. 2022) has opened the possibility of reconstructing many complete MAGs from a microbial sample and thus analyzing their diversity indices. Figure 4 shows great variation...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...that enables improved recovery from metas through de-replication. ISME J 11: 2864–2868. doi:10.1038/ismej.2017.126 ↵Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial s recovered from isolates, single cells, and metas. Genome Res 25: 1043–1055. doi:10...
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Research: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules
- Jonathon L. Baker,
- James T. Morton,
- Márcia Dinis,
- Ruth Alvarez,
- Nini C. Tran,
- Rob Knight,
- and Anna Edlund
Genome Res. January 2021 31: 64-74; Published in Advance November 25, 2020, doi:10.1101/gr.265645.120
...the completion (D), N50 (E), contamination (F), and contigs/Mbp (G) of the SGBs, GGBs, and FGBs. Completion and contamination were determined by CheckM (Parks et al. 2015). Statistically significant differences between groups were determined using a Tukey's multiple comparisons posttest following a one-way ANOVA...
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Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
- Bin Zhao,
- John A. Lees,
- Hongjin Wu,
- Chao Yang,
- and Daniel Falush
Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
..., Tyson GW. 2015. CheckM: assessing 585 the quality of microbial s recovered from isolates, single cells, and 586 metas. Genome Res 25: 1043-1055. 587 Power RA, Parkhill J, de Oliveira T. 2017. Microbial -wide association studies: 588 lessons from human GWAS. Nat Rev Genet 18: 41-50. 589 Price MN, Dehal...
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