AMOS

The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler. Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.

Quick links:

• AMOS Getting Started
• Download
• SourceForge project page

Announcements

• August 5, 2011 - Version 3.1.0 of AMOS released!
• August 2, 2011 - AMOS Sample Data posted
• December 7, 2010 - Version 3.0.0 of AMOS released!

Documentation

Assemblers

• AMOScmp - comparative assembler
• AMOScmp-shortReads - comparative assembler for short reads (Solexa,454)
• AMOScmp-shortReads-alignmentTrimmed - comparative assembler for short reads that uses alignment based trimming
• minimus - basic genome assembler for small datasets
• Minimo - the minimus assembler with many more options: short read support, variable stringency, strand-specificity, various outputs formats
• minimus2 - basic genome assembler for two datasets; can also be used as an assembly merge pipeline
• minimus2-blat - Same as minimus2 but uses BLAT instead of Nucmer for added speed

Validation and Visualization

• Hawkeye - assembly viewer
• amosvalidate - assembly forensics
• FRCurve - Feature-Response Curve
• Benchmark - assembly benchmark data

Scaffolding

• Bambus - Open source standalone hierarchical scaffolding
• Bambus2 - Scaffolding Polymorphic Genomes and Metagenomes

Trimming, Overlapping, & Error Correction

• Figaro - statistical vector trimmer
• UMD Overlapper - High quality overlap computations
• KI Overlapper - Repeat aware overlapper
• AutoEditor - Automatic correction of genome sequencing errors
• FastqQC - Read composition and quality

Utilities

• File conversion utilities - converting data to and from AMOS
• AMOS Utilities - general utilities
• runAmos - Pipeline executor

AMOS Development

• Programmer's guide - Getting started with the Source code
• Infrastructure - Developer level details
• Wiki guide - Guide for editing the wiki

Assembly Tutorials

• Assembly primer - overview of genome assembly.
• Representing assemblies (not just in AMOS)
• Running Celera Assembler

Additional documentation in development through the AMOS Documentation Project

Download

The AMOS source if freely available for download from the File Release Section of our SourceForge project page. Please refer to the COPYING license included in the package for a description of the Artistic License, the same OSI certified open source license used by Perl and countless other packages. Not all of the above packages are included with the standard AMOS distribution, please see the homepage for the software you wish to download to verify that it is included with the AMOS source distribution.

Download from SourceForge

Consortium members

There have been numerous positive responses regarding the AMOS initiative, and we expect the list of involved organizations to grow significantly as the project matures. Please contact us if you want to join. The groups currently involved with the development of AMOS are listed below, along with their responsibilities and areas of expertise.

• University of Maryland, Center for Bioinformatics and Computational Biology
  • project organization and direction
  • infrastructure
  • consensus
  • automated sequence editing
  • scaffolding
  • overlap detection
  • contig construction

• The Institute for Genomic Research
  • production pipelines
  • automated finishing tools
  • error correction

• Karolinska Institutet
  • overlap detection
  • error correction

• Marine Biological Laboratory - Woods Hole
  • graphical interface
  • integration of assembly data with analysis (gene, polymorphism, etc.) information

Join the consortium

All interested parties are welcome to join or aid the AMOS consortium. Please address all correspondence via Email to:

amos-help (at) lists (dot) sourceforge (dot) net

To receive information regarding new releases and developments, please subscribe to our moderated, low-traffic users' mailing list:

amos-users (at) lists (dot) sourceforge (dot) net

Bug reports and support

For AMOS bug reports or support requests, please browse our SourceForge project page or Email us at:

amos-help (at) lists (dot) sourceforge (dot) net

Acknowledgements

The AMOS consortium would like to thank the following organizations for their funding and/or support:

• The National Institutes of Health - grants R01-LM06845, N01-AI-15447
• The National Science Foundation - grants IIS-9902923, IIS-9820497
• Department of Homeland Security - cooperative agreement W81XWH-05-2-0051
• SourceForge.net