AMOS documentation project


This is the homepage for a project to develop a collection of detailed documents describing the various components of the AMOS package.  If you are interested in participating in this project please contact mpop [at] umiacs.umd.edu .  Also, if  you are interested in helping out with the development of AMOS, check out the AMOS wants and needs page (hint to UMD undergrads looking for a programming job).  Particularly relevant to the documentation project is the need for an automated mechanism for extracting documentation from the help messages produced by the various AMOS programs.  

Tutorials

Assembly primer - overview of genome assembly.

Step-by-step instructions for using various components of AMOS.

AMOS: getting started
Programmer's guide
Representing assemblies (not just in AMOS)
Running Celera Assembler (i.e. how to use the various runca.* scripts distributed with AMOS)

Conversion tools

How to convert to and from the various AMOS formats

Conversion tool overview

AMOS utilities

Documentation for some useful AMOS utilities.  

All of AMOS

When we get to this, we'll have here documentation for all programs in the AMOS bin/ directory.