ADiR: Assembler for Di-base Reads

ADiR is an assembler for AB SOLiD colorspace reads that makes use of color transition properties in resolving overlap and consensus.

Please direct correspondence to adir-project at cs dot utoronto dot ca.

Recent News
ADiR version 0.3.5 released Tim Smith 2009-07-22 This release contains the following updates: - New "filter" program to filter short / low quality contigs - Added "-1" flag to "overlapper" for processing reads from a single strand - Converted "colorconsensus" to use default values when none are given - Added default value printing to all programs Get the new source release here: http://solidsoftware...
ADiR version 0.3.1 released Tim Smith 2009-07-02 This release fixes some alignment layout bugs. Get the 0.3.1 ADiR source release from http://solidsoftwaretools.com/gf/download/frsrelease/175/738/adir-0.3.1.tar.gz
ADiR version 0.3.0 released Tim Smith 2009-06-22 This version includes improved bubble/splinter removal. Get the ADiR source release from: http://solidsoftwaretools.com/gf/download/frsrelease/174/737/adir-0.3.0.tar.gz
ADiR version 0.2.5 released Tim Smith 2009-06-05 This release includes two major performance enhancements: k-mer hashing and improved splinter removal. This release also fixes a bug in contig layout that was causing incorrect alignments and consensus caller segfaults. Get the ADiR source release from http://solidsoftwaretools.com/gf/download/frsrelease/173/724/adir-0.2.5.tar.gz
ADiR version 0.2.0 released Tim Smith 2009-05-28 This version includes a completely re-written overlapper. See the README file for new usage information. Get the ADiR source release from http://solidsoftwaretools.com/gf/download/frsrelease/172/719/adir-0.2.0.tar.gz

Time	Activity Type	By
2009-Jul-22
13:56:03	Commit: Updated sample assembly script	Tim Smith
13:54:59	Commit: Added default values to colorconsensus; added printing of defaults to all programs	Tim Smith
2009-Jul-21
15:50:33	Commit: Added filter program, slight usablility changes to colorconsensus	Tim Smith
2009-Jul-02
15:27:38	Commit: Layout bug fixes, version bump	Tim Smith
2009-Jun-22
15:52:14	Commit: Fixed layout bug	Tim Smith
09:19:00	Commit: Version 0.3.0 - improved splinter/bubble removal	Tim Smith
2009-Jun-09
16:32:39	Commit: Performance enhancements, stats printing	Tim Smith
2009-Jun-04
15:58:34	Commit: Turned off debug flag	Tim Smith
15:57:52	Commit: Bugfixes in overlapper; first bits of quality value handling code in	Tim Smith
10:29:44	Commit: Cleaned up csutils	Tim Smith
2009-Jun-03
15:10:42	Commit: Added fasta and util source files	Tim Smith
2009-Jun-02
17:26:52	Commit: Performance enhancements (kmer filter and splinter removal loop redesign); Some code cleanup in the overlapper.	Tim Smith
2009-May-28
12:15:33	Commit: Updated README, bumped version number	Tim Smith
12:02:11	Commit: Removed old collapser / clip code	Tim Smith
11:55:49	Commit: Updated sample assemble script	Tim Smith

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Description
An assembler for colorspace reads that makes use of color transition properties in resolving overlap and consensus.
Developer Info
Michael Brudno Tim Smith Taisija Santare
Trove Categorization
Development Status: 3 - Alpha Intended Audience: Developers, End Users/Desktop License: GNU General Public License (GPL) V3 Operating System: Linux, Linux 64 Bit, MacOS, POSIX Programming Language: C, C++, Python, Unix Shell Spoken Language: English Topic: Bio-Informatics

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ADiR: Assembler for Di-base Reads

ADiR: Assembler for Di-base Reads