The analysis of these vast amounts of data is complicated by the fact that reconstructing large genomic segments from metagenomic reads is a formidable computational challenge. Even for single organisms, the assembly of genome sequences from sequencing reads is a complex task, primarily due to ambiguities in the reconstruction that are caused by genomic repeats. In metagenomic data, additional challenges arise from the non-uniform representation of genomes in a sample as well as from the genomic variants between the sequences of closely related organisms.


assembly and analysis toolkit for metagenomics

metAMOS is an integrated assembly and analysis pipeline for metagenomic data. It is built around the Bambus2 metagenomic scaffolder and includes many current tools for assembly, gene finding, and taxonomic classification. metAMOS is under active development and changes quite frequently

Obtaining metAMOS


Metastats is software for detecting differentially abundant features in metagenomic case/control studies. It is the first tool developed in the context of metagenomic data comprising multiple samples, and relies on a non-parametric t-test. This software is no longer current, not recommended for use, and is not being provided anymore. Newer tools exist in this space, such as metagenomeseq, corncob, and others.

Genomic Variation

Graphs to Diversity: extracting genomic variation from sequence graphs

Sequencing as a tool for uncovering genome variation

Principal Investigators

Metagenomic Assembly

Assembly and Analysis Software for Exploring the Human Microbiome

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Gene Finding

Metagenomic assembly

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VALET - VALidating mETagenomic assemblies

VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the assembly, the depth of coverage is fairly uniform along contigs, etc.). The violations of these invariants are reported allowing one to pinpoint areas that were potentially mis-assembled, or to compare the quality of different assemblies.

Metagenomic data analysis

Metagenomics is a new field of research in which scientists analyze the genomes of organisms recovered directly from the environment. Most naturally occuring bacteria cannot be cultured and therefore cannot be analyzed by traditional means. Metagenomic studies provide us with a mechanism for analyzing previously unknown organisms. At the same time we can examine the diversity of organisms present in specific environments as well as analyze the complex interactions between members of a specific environment. While most metagenomic studies

Principal Investigators

Modeling microbial communities

Principal Investigators

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