The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
Open accessAbstract
Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed $1$ billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under $7$ h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of $30$ in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores. EPA-NG is available under the AGPLv3 license: https://github.com/Pbdas/epa-ng.
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Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., et al. (2015) · Science · doi:10.1126/science.1261359 · Cited by 2,921
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Metagenomic species profiling using universal phylogenetic marker genes
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Self-citationThe Closest BLAST Hit Is Often Not the Nearest Neighbor
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Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests
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Meta‐Analysis of Gut Dysbiosis in Parkinson's Disease
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Unifying the known and unknown microbial coding sequence space
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2022) · eLife · doi:10.7554/elife.67667 · Cited by 134
Metadata
- Authors
- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., Darriba, D., Flouri, T., & Stamatakis, A.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-09-21
- Volume
- 68
- Issue
- 2
- Pages
- 365-369
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2951358594
- Cited by
- 687
- References
- 14
- FWCI
- 15.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
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