User contributions
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- 22:34, 7 July 2009 (diff | hist) . . (+1,610) . . N KI Overlapper (New page: == Overview == The Karolinska Institutet overlapper is designed to handle the problems created by sequencing errors. Instead of exact k-mer matches - the approach used by most existing as...) (current)
- 22:33, 7 July 2009 (diff | hist) . . (+86) . . UMD Overlapper (current)
- 22:32, 7 July 2009 (diff | hist) . . (+1,206) . . N UMD Overlapper (New page: == Overview == The UMD overlapper is designed to reduce the number of overlaps produced by the assembler by reducing the number of repeat-induced overlaps. Furthermore the algorithm is gr...)
- 22:31, 7 July 2009 (diff | hist) . . (+1) . . AMOS
- 22:30, 7 July 2009 (diff | hist) . . (+124) . . AMOS
- 22:28, 7 July 2009 (diff | hist) . . (+4,014) . . N Infrastructure (New page: The principal benefit of the AMOS project is its modular design, but in order to facilitate many, isolated components, a robust infrastructure is desirable. In response to this need, TIGR ...)
- 22:23, 7 July 2009 (diff | hist) . . (+16) . . Benchmark (current)
- 22:21, 7 July 2009 (diff | hist) . . (+4,484) . . N Benchmark (New page: == Overview == We have assembled a set of benchmark assembly genomes. Each benchmark set comes with the sequence of the finished genome, random shotgun reads, closure reads, and ancillary...)
- 22:14, 7 July 2009 (diff | hist) . . (+219) . . AMOS
- 22:06, 7 July 2009 (diff | hist) . . (+619) . . N Figaro (New page: == Overview == Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence. By statistically modeling shor...)
- 21:54, 7 July 2009 (diff | hist) . . (+2,867) . . N File conversion utilities (New page: == Overview == The ASM File converters are a collection of utilities for converting sequence and assembly data between the most widely used data formats as well as to and from the AMOS me...)
- 21:45, 7 July 2009 (diff | hist) . . (+706) . . N AutoEditor (New page: == Overview == The AutoEditor is a tool developed at TIGR that combines the trace information with the tiling of reads within a contig in order to identify and correct sequencing errors. ...)
- 21:43, 7 July 2009 (diff | hist) . . (+1,443) . . N Bambus (New page: == Overview == Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly pr...)
- 21:36, 7 July 2009 (diff | hist) . . (-10) . . Amosvalidate
- 21:02, 7 July 2009 (diff | hist) . . (+9) . . Amosvalidate
- 20:57, 7 July 2009 (diff | hist) . . (-2) . . Amosvalidate
- 20:56, 7 July 2009 (diff | hist) . . (-3) . . Amosvalidate
- 20:54, 7 July 2009 (diff | hist) . . (+12,318) . . N Amosvalidate (New page: Automated assembly validation pipeline. Adam Phillippy, Michael Schatz, Mihai Pop Center for Bioinformatics and Computational Biology, University of Maryland Publication: Genome assemb...)
- 20:54, 7 July 2009 (diff | hist) . . (+1,572) . . N Hawkeye (New page: An Interactive Visual Analytics Tool for Genome Assemblies. Michael Schatz - Adam Phillippy Ben Shneiderman - Steven Salzberg Version 1.0 - March 5, 2007 Publication: Schatz, M.C., P...)
- 20:43, 7 July 2009 (diff | hist) . . (+2,394) . . N AMOScmp-shortReads-alignmentTrimmed (New page: == Overview == AMOScmp-shortReads-alignmentTrimmed is a modified version of AMOScmp designed for alignment based trimming and assembling of short reads. Differences compared to AMOScmp: ...) (current)
- 20:40, 7 July 2009 (diff | hist) . . (+1,175) . . N AMOScmp-shortReads (New page: == Overview == AMOScmp-shortReads is a modified version of AMOScmp designed for assembling short reads. Differences compared to AMOScmp: * uses a smaller nucmer alignment cluster size * u...) (current)
- 20:38, 7 July 2009 (diff | hist) . . (+1,883) . . N AMOScmp (New page: == Overview == A comparative assembler is a program that can assemble a set of shotgun reads from an organism by mapping them to the finished sequence of a related organism. Thus, a compa...) (current)
- 21:17, 3 June 2009 (diff | hist) . . (-15) . . Minimus2
- 21:17, 3 June 2009 (diff | hist) . . (+1,781) . . N Minimus2 (New page: == Overview == minimus2 is a modified version of the minimus pipeline designed for merging one or two sequence sets (S1,S2). It uses a nucmer based overlap detector which is much faster t...)
- 20:54, 3 June 2009 (diff | hist) . . (+22) . . Minimus
- 20:53, 3 June 2009 (diff | hist) . . (-1,093) . . Minimus
- 20:52, 3 June 2009 (diff | hist) . . (-518) . . Minimus
- 20:49, 3 June 2009 (diff | hist) . . (+48) . . Minimus
- 20:49, 3 June 2009 (diff | hist) . . (-3) . . Minimus
- 20:47, 3 June 2009 (diff | hist) . . (+3,369) . . N Minimus (New page: == Overview == minimus is an assembly pipeline designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemb...)
- 20:43, 3 June 2009 (diff | hist) . . (0) . . AMOS Documentation Project
- 20:42, 3 June 2009 (diff | hist) . . (+1,310) . . N AMOS Documentation Project (New page: 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 proj...)
- 20:37, 3 June 2009 (diff | hist) . . (+5) . . Programmer's guide
- 20:36, 3 June 2009 (diff | hist) . . (+33) . . Programmer's guide
- 20:35, 3 June 2009 (diff | hist) . . (+12,583) . . N Programmer's guide (New page: == Getting AMOS == AMOS can be downloaded from our Sourceforge download site: http://sourceforge.net/project/showfiles.php?group_id=134326 as a tar file, or directly from the AMOS CVS (see...)
- 20:29, 3 June 2009 (diff | hist) . . (+1) . . AMOS Getting Started
- 20:28, 3 June 2009 (diff | hist) . . (+194) . . AMOS Getting Started
- 20:24, 3 June 2009 (diff | hist) . . (-22) . . AMOS Getting Started
- 20:21, 3 June 2009 (diff | hist) . . (+18,111) . . N AMOS Getting Started (New page: {| align="right" | __TOC__ |} == Introduction == Is AMOS an assembler? is one of the first questions we are asked. The short answer is no. AMOS is not an assembler, rather a softwa...)
- 20:10, 3 June 2009 (diff | hist) . . (+1) . . AMOS
- 18:03, 3 June 2009 (diff | hist) . . (+72) . . AMOS
- 18:01, 3 June 2009 (diff | hist) . . (+88) . . AMOS (→Download)
- 18:00, 3 June 2009 (diff | hist) . . (-21) . . AMOS
- 17:59, 3 June 2009 (diff | hist) . . (+3,583) . . AMOS
- 20:20, 2 June 2009 (diff | hist) . . (+711) . . N AMOS (New page: 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-Sour...)
- 20:19, 2 June 2009 (diff | hist) . . (+4) . . N MediaWiki:Mainpage (New page: AMOS) (current)
- 20:17, 2 June 2009 (diff | hist) . . (+597) . . N Wiki guide (New page: <big>'''MediaWiki has been successfully installed.'''</big> Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. == Getting...)
- 20:16, 2 June 2009 (diff | hist) . . (0) . . File:MediaWikiSidebarLogo.png (uploaded a new version of "Image:MediaWikiSidebarLogo.png") (current)
- 20:10, 2 June 2009 (diff | hist) . . (0) . . File:MediaWikiSidebarLogo.png (uploaded a new version of "Image:MediaWikiSidebarLogo.png")
- 20:08, 2 June 2009 (diff | hist) . . (0) . . N File:MediaWikiSidebarLogo.png
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