NEWS

Welcome to AMOS Assembler. A Modular Open Source Assembler.
website: <http://amos.sourceforge.net>
contact: <amos-help@lists.sourceforge.net>

AMOS Assembler NEWS
===================
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.


Version Release History
=======================

Version 3.1.0 - August 2011
     * Versioning of AMOS Banks -- all old banks require rebulding
     * Sample data available at: http://sourceforge.net/projects/amos/files/sample_data/
     * Added FRCurve pipeline for comparing multiple assemblies of the same data: http://amos.sf.net/frcurve/
     * New version of Hawkeye using Qt 4 (removed Qt 3 version completely)
     * make-consensus now handles ambiguous N bases (reported by Mark Rose).
     * Moved undocumented/prototype code into Experimental directory. Use configure --enable-Experimental to build
     * Many small updates and bug fixes

Version 3.0.0 - December 2010

     * New version of the scaffolder, Bambus 2.0
     * New lightweight, parametrable assembler based on Minimus, Minimo
     * Experimental support for Qt 4 in Hawkeye
     * Updated unitigger for Minimus, Unitigger
     * Compute the complexity of a genome with genome-complexity (http://www.biomedcentral.com/1471-2105/11/21)
     * Utility that can convert large fastq files into a bank, fast2amos
     * Ability to build only core AMOS binaries with Autoconf
     * Support for writing SAM format in bank2contig
     * toAmos now automatically reads mate pairs in FASTA files (reads ending in /1 or .1)
     * libSlice - correctly compute consensus even with very deep coverage
     * Many small updates and bug fixes

Version 2.0.5 - March 2008

     * `amosvalidate' assembly validation pipeline released

Version 1.3.1 - June 2005

     * minor release for OSX Tiger and GCC 4.0 compatibility
     * `AMOScmp' administrative updates

Version 1.3.0 - May 2005

     * `bankViewer' first version released
        * provides GUI interface for AMOS bank browsing
     * `libAMOS'
        * Matepair_t replaced with extra field in Fragment_t
        * Group_t added for object groups
        * Link_t added for general object links
        * Edge_t added for general object edges
        * Index_t added for object IID indexing
        * Feature_t object modifed to be more general
        * Universal_t gained extra status char
        * ReverseComplement() method added
     * `tigger' efficiency enhancement
     * `AmosFoundation.pm' added
     * `libread' Staden trace IO library packaged

Version 1.2.9 - February 2005

     * `tarchive2amos' bug fixes
     * `amos2ace' bug fixes
     * `hash-overlap' self-overlap bug fixed
     * `tigger' now ignores self-overlaps

Version 1.2.8 - January 2005

     * `minimus'
        * circular contig bug fixed
        * layout bug fixed
        * multiple overlaps between two reads bug fixed
     * `libAMOS'
        * Bank_t map partition now a plaintext tab-delimited file
        * Message_t read() bug fixed
        * IDMap_t remove() bug fixed
        * BankStream_t operator()>> bug fixed
     * `bank-unlock' and `bank-clean' utilities added
     * `bank-*' tools now report progress
     * `toAmos' bug fix
     * `tarchive2amos' bug fix
     * `amos2ace' bug fix

Version 1.2.7 - November 2004

     * `AMOScmp'
        * improved conflict resolution
        * operates on an AMOS bank
     * `libAMOS'
        * Feature_t added to Contig_t and Scaffold_t
        * BankSet_t, BankStreamSet_t, UniversalSet_t added
        * read/write locks added to Bank_t
        * Message_t iterator added
     * documentation updated

Version 1.2.6 - September 2004

     * `minimus' negative offset bug fixed
     * `make-consensus' ID swapping bug fixed
     * `AMOScmp' won't bomb if mate information absent from the bank

Version 1.2.5 - September 2004

     * Added `minimus' pipeline for lightweight assembly tasks.
     * Improved portablity.
     * Added --enable-FEATURE options to configure for conditional
       builds.

Version 1.2.3 - August 2004

     * First official release of the AMOS distribution, much work
       yet to be done.
     * Added `AMOScmp' comparative assembly pipeline.