MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
| Autor: | Huson, Daniel H., Beier, Sina, Flade, Isabell, Górska, Anna, El-Hadidi, Mohamed, Mitra, Suparna, Ruscheweyh, Hans-Joachim, Tappu, Rewati |
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| Přispěvatelé: | Poisot, T |
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
Computer and Information Sciences
QH301-705.5 Sequence Databases DNA cloning Microbial Genomics Research and Analysis Methods Microbiology Computer Software Database and Informatics Methods User-Computer Interface Mathematical and Statistical Techniques Genetics Biology (General) Molecular Biology Techniques Sequencing Techniques Molecular Biology Taxonomy Data Management Shotgun Sequencing Microbiota Biology and Life Sciences High-Throughput Nucleotide Sequencing Genomics Sequence Analysis DNA Biological Databases Medical Microbiology Metagenome Microbiome Metagenomics Sequence Analysis Sequence Alignment Functional Analysis Genome Bacterial Software Research Article Cloning |
| Zdroj: | PLoS Computational Biology PLoS Computational Biology, Vol 12, Iss 6, p e1004957 (2016) |
| ISSN: | 1553-7358 1553-734X |
| Popis: | There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce Author Summary Microbiome sequencing projects continue to grow rapidly, both in the number of samples considered and sequencing reads collected. With MEGAN Community Edition (CE), we provide a highly efficient program for interactive analysis and comparison of such data, allowing one to explore hundreds of samples and billions of reads. While taxonomic profiling is performed based on the NCBI taxonomy, we provide a number of different functional profiling approaches such as SEED, eggNOG, KEGG, and a new InterPro2GO classification scheme. MEGAN CE also supports the use of metadata in the context of principal coordinate analysis and clustering analysis. |
| Databáze: | OpenAIRE |
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