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ToolsBenoit, Gaëtan, Raguideau, Sébastien, James, Robert, Phillippy, Adam M., Chikhi, Rayan and Quince, Christopher (2024) High-quality metagenome assembly from long accurate reads with metaMDBG. Nature Biotechnology, 42 (9). pp. 1378-1383. ISSN 1087-0156
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Abstract
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids.
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| Additional Information: | Data availability statement: All data sets used in this study were downloaded from the NCBI Sequence Read Archive; accession numbers are given in Supplementary Table S1. Zymo-HiFi mock reference genomes are available at https://s3.amazonaws.com/zymo-files/BioPool/D6331.refseq.zip. ATCC mock reference genomes are available at https://www.atcc.org/products/msa-1003. Code availability statement: MetaMDBG is available at https://github.com/GaetanBenoitDev/metaMDBG. The analysis scripts used in this study to compare assemblers are available at https://doi.org/10.5281/zenodo.8321179. Funding Information: C.Q., S.R. and G.B. acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation; Earlham Institute Strategic Programme Grant (Decoding Biodiversity) BBX011089/1 and its constituent work package BBS/E/ER/230002C; the Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work packages BBS/E/T/000PR9818 and BBS/E/T/000PR9817; and the Core Capability Grant BB/CCG2220/1. S.R. is also funded through National Environmental Research Council (NERC) grant ResPharm (NE/T013230/1). C.Q. was also partially funded by Medical Research Council (MRC) Methodology Grant \u2018Strain resolved metagenomics for medical microbiology\u2019 MR/S037195/1. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under Marie Sk\u0142odowska-Curie grant agreement Nos. 872539 and 956229 (R.C.). R.C. was supported by ANR Transipedia, SeqDigger, Inception and PRAIRIE grants (ANR-18-CE45-0020, ANR-19-CE45-0008, PIA/ANR16-CONV-0005, ANR-19-P3IA-0001). A.M.P. was supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (NIH). We acknowledge the NIH Intramural Sequencing Center (NISC) for assistance with PacBio sequencing. We would also like to thank S. Nurk for stimulating discussions during the course of this study and O. Soyer for supervising the collection of the anaerobic digester samples through BBSRC project BB/N023285/1. We thank the editor for constructive comments on earlier versions of the manuscript. |
| Uncontrolled Keywords: | biotechnology,bioengineering,applied microbiology and biotechnology,molecular medicine,biomedical engineering ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 10:30 |
| Last Modified: | 23 Oct 2024 10:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97134 |
| DOI: | 10.1038/s41587-023-01983-6 |
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