MEGAN pipeline

MEGAN specifications


Unique identifier OMICS_01516
Alternative names MEtaGenome ANalyzer, MEGAN6, MEGAN5
Software type Package/Module, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 6.8.14
Stability Stable
Maintained Yes


  • MEGAN-LR (Long Read extension of the metageno



Add your version



  • person_outline Daniel H. Huson <>
  • person_outline Benjamin Albrecht <>
  • person_outline Caner Bagci <>
  • person_outline Irina Bessarab <>

Additional information

A free edition (Community Edition) and a paid edition (Ultimate Edition) are both available.

Publications for MEtaGenome ANalyzer

MEGAN citations

PMCID: 5830625

[…] sequence reads were mapped against known nucleotide sequences in the database including microbial genomes using megablast programs. to summarize taxonomic information, the metagenomic browser megan6 community edition (university of tübingen, tübingen, germany) was used27. after low accuracy reads (bit score <250), unclassified reads, and illumina sequencing spike-in phix reads […]

PMCID: 5701178

[…] to show hierarchical clustering of fly species based on their microbiome. species diversity index shannon-weaver68 was calculated using ‘species’ level of ncbi taxonomy to generate a table with megan 566. permanova and anova statistical analysis were performed with phyloseq.69, as implemented in the tool microbiomeanalyst70. venn diagrams were generated with biovenn71 using the ‘species’ […]

PMCID: 5171636

[…] ncbi-nr database (downloaded 15.10.15) were carried out for the assembled contigs of each reference transcriptome, with an e-value cut off of 1e-04. the results of the blastx surveys were fed into megan v5.10.650 for comparative taxonomic analysis. to compare the assigned taxonomic content of the assembled contigs from the malacosteus and pachystomias retinal tissue, the overall number […]

PMCID: 5028885

[…] yielding approximately 180 million read pairs. low confidence reads were removed, and the identify of bacteria present in the tick microbiome were determined utilizing ≥1 kb contigs binned using megan19., trimmed reads were assembled into contigs using idba-ud20, and by comparing them to francisella genome sequences, fle contigs were identified. all trimmed reads were mapped to these contigs […]

MEGAN institution(s)
Center for Bioinformatics, University of Tübingen, Tübingen, Germany

MEGAN review

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Works well with DIAMOND for metatranscriptomic data analysis.