Integrative analysis of environmental sequences using MEGAN4.

By Daniel H. Huson, S. Mitra, H. Ruscheweyh, N. Weber, Stephan C. Schuster. Genome Research, 2011

1,524 citations recorded by the source corpus.

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c55c3c9492ffd9aea9099f54af5d69b669387933

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Citations in the corpus

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses (2014, neutral): “0 [72].”
Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem (2017, methodology): “We assigned a taxonomic name to each OTU sequence using blastn (Camacho et al., 2009) on a local version of the full NCBI nucleotide database (current as of July 2016), recovering up to 50 hits per query sequence and reconciling conflicts among equally good matches using the last common ancestor app”
Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples (2012, neutral): “Taxon identification was made using MEGAN 4 [50], with following LCA settings: Min.”
Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide (2013, methodology): “For a schematic overview of the phylogenetic composition and diversity across samples, BLAST results can be imported and viewed in the program MEGAN (Huson et al., 2011).”
METAGENassist: a comprehensive web server for comparative metagenomics (2012, methodology): “One other metagenomics program (MEGAN) does provide limited (eight categories) taxonomic-tophenotypic mapping for the creation of bar charts and pie charts.”
Illumina metabarcoding of a soil fungal community (2013, methodology): “We parsed the BLAST outputs in MEGAN 4 (Huson et al., 2011) for taxonomic assignment (min. support: 1, min. score: 200, top percent: 5), and we retained clusters with supported fungal origin.”
Soil metagenomics reveals differences under conventional and no-tillage with crop rotation or succession (2013, methodology): “Data analyses Sequences were analyzed with the MEGAN4 software (Huson et al., 2011), based on the comparison of BLASTX with all the R.C. Souza et al. / Applied Soil Ecology 72 (2013) 49– 61 51 Table 1 Soil chemical and granulometrica properties in the 0–10 cm layer.”
Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil (2016, methodology): “nt BLAST matches were fed into MEGAN v5 (Huson et al. 2011) to com-”