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. MetAMOS was designed with efficiency in mind and can run through tens of millions of reads in a few hours on a multi-core workstation with ample RAM.

Research project: 
UMIACS Investigators: 
External Collaborators: 
Todd Treangen
Sergey Koren