Searching journal content for articles similar to Parks et al..

Displaying results 1-6 of 6

For checked items

view abstracts
download to citation manager

Select this article
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...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
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...
Select this article
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...
Select this article
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...
ACCEPTED MANUSCRIPT

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Parks et al..

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: