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Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
- Ali Azizpour,
- Advait Balaji,
- Todd J. Treangen,
- and Santiago Segarra
Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
...: assembly graph constructionIn the initial step, we construct an assembly graph in order to leverage graph features for repeat detection. To do so, we assemble the input reads to contigs and obtain the assembly graph as illustrated in Figure 2A. Here, we use the popular metagenomic assembler, metaSPAdes...
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RECOMB 2022 Special/Methods: Assembler artifacts include misassembly because of unsafe unitigs and underassembly because of bidirected graphs
- Amatur Rahman and
- Paul Medvedev
Genome Res. September 2022 32: 1746-1753; Published in Advance July 27, 2022, doi:10.1101/gr.276601.122
..., Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27: 824–834. doi:10.1101/gr.213959.116 ↵Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, et al. 2022. The complete sequence of a human . Science 376: 44–53. doi:10...
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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
...of metaplasmidSPAdes. From a practical perspective, metaplasmidSPAdes introduces an unnecessary dependency on the metaSPAdes assembler.Application of our approach to 32 environmental samples uncovered 20 clades of ecMGEs (primarily gut and sewage plasmids), showcasing the strength of metagenomic approaches...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...extraordinarily high Nubeam within-sample diversities. We thus performed de novo assembly using state-of-the-art metagenomics assembler metaSPAdes (Nurk et al. 2017) for all unmapped reads to produce contigs (minimum length 228 bp) and remapped reads to contigs. To our surprise, 54% of the reads fail...
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Method: Plasmid detection and assembly in genomic and metagenomic data sets
- Dmitry Antipov,
- Mikhail Raiko,
- Alla Lapidus,
- and Pavel A. Pevzner
Genome Res. June 2019 29: 961-968; Published in Advance May 2, 2019, doi:10.1101/gr.241299.118
...and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 28: 565–591. doi:10.1128/CMR.00116-14 ↵Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27: 824–834. doi:10.1101/gr.213959.116 ↵Ondov BD...
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Method: BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs
- Dmitry Meleshko,
- Hosein Mohimani,
- Vittorio Tracanna,
- Iman Hajirasouliha,
- Marnix H. Medema,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. August 2019 29: 1352-1362; Published in Advance June 3, 2019, doi:10.1101/gr.243477.118
...: assembling genomic/metagenomic reads with SPAdes/metaSPAdes; identifying domain-edges in the assembly graph; extracting BGC subgraphs from the assembly graph; restoring collapsed domains in the assembly graph; constructing the scaffolding graph; and constructing putative BGCs by solving the Rural Postman...
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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
...Ecol 52: 443–454. doi:10.1111/1365-2664.12380 ↵Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27: 824–834. doi:10.1101/gr.213959.116 ↵O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith...
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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
...reads alone remains challenging: Short-read metagenomic studies rarely result in the complete assembly of even a single meta-assembled (MAG) (Nurk et al. 2017). The recent emergence of the long and accurate Pacific Biosciences (PacBio) high-fidelity (HiFi) reads (Wenger et al. 2019) has led to the era...
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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
...for circularization (see below). The single scaffold should be checked for complete coverage and support of the consensus. Gaps or local assembly errors must be dealt with before the is classified as curated and complete (some additional checks are described below).Some assemblers (e.g., IDBA-UD, metaSPAdes) retain...
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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
...://github.com/biobakery/kneaddata). De novo assembly of the metas was performed using metaSPAdes (Nurk et al. 2017), and a separate assembly was performed for each sample. The resulting assemblies were binned using MetaWRAP (Uritskiy et al. 2018). fastANI (Jain et al. 2018) was used to dereplicate highly similar bins (≥95% ANI), likely...

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