Genome/Metagenome Assembly


Metagenomic datasets prove challenging to assemble using traditional assembly pipelines designed for individual genomes. Using AMOS as a foundation, we have created a robust & easy-to-use metagenomic assembly pipeline that takes reads (FASTA,FASTQ,SFF) and assembles them into Unitigs (CABOG,NEWBLER,Minimus,SOAPdenovo), Contigs & Scaffolds (Bambus2) & ORFs (Glimmer MG, MetaGeneMark), and annotates results using Metaphyler and a graph-based propagation method.

AMOS Assembler project

The is a set of tools, libraries, and freestanding genome assemblers, all open source. AMOS is also an open consortium that includes TIGR, the University of Maryland, The Karolinska Institutet, and the Marine Biological Laboratory.


is a comparative genome assembler, which uses one genome as a reference on which to assemble another, closely related species. See the journal paper here.

III: Small: Genome Assembly Using Sparse Sequence Info

Rapid advances in DNA sequencing technologies are providing scientists with the ability to rapidly and cost-effectively decode the genomes of organisms. Current technologies, however, can only reconstruct a fragmented picture of a genome's chromosomes. Stitching the resulting fragments together into a complete genome currently requires costly and time-intensive laboratory experiments.

Principal Investigators

Algorithms for the Analysis of Data from Massively-parallel Genome Sequencing

New generation DNA sequencing technologies are revolutionizing modern biological research. Scientists can now generate the rough equivalent of an entire human genome (~3 billion base-pairs of DNA) in just a few days with one single sequencing instrument. Until recently, such amounts of data could only be generated at large genome centers using hundreds of sequencers. The analysis of these data is complicated by their size - a single run of a sequencing instrument yields terabytes of information, often requiring a significant scale-up of the existing computational infrastructure.

Principal Investigators


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