AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contiging, and assembly manipulation.
AMOS is composed of a number of modules, each of which performs a step in the assembly process. While each module can be run individually, AMOS provides a module that controls the entire pipeline assembly, called runAmos.
To run this software interactively in a Linux environment run the commands:
module load amos
runAmos [options] -c <config>
where <config> is a configuration file specifying various parameters. To view the available options for runAmos, use the following command: