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Critical assessment of metagenome interpretation − a benchmark of computational metagenomics software
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(2017) Critical assessment of metagenome interpretation − a benchmark of computational metagenomics software. Working Paper. bioRxiv: Cold Spring Harbour Laboratory. (Unpublished) Research output not available from this repository, contact author.
Official URL: http://dx.doi.org/10.1101/099127
Abstract
In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.
| Item Type: | Working or Discussion Paper (Working Paper) | ||||
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| Divisions: | Faculty of Medicine > Warwick Medical School > Biomedical Sciences Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Medicine > Warwick Medical School |
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| Publisher: | Cold Spring Harbour Laboratory | ||||
| Place of Publication: | bioRxiv | ||||
| Book Title: | Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software | ||||
| Official Date: | 12 June 2017 | ||||
| Dates: |
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| DOI: | 10.1101/099127 | ||||
| Institution: | University of Warwick | ||||
| Status: | Not Peer Reviewed | ||||
| Publication Status: | Unpublished | ||||
| Access rights to Published version: | Open Access | ||||
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