User contributions
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- 18:47, 8 July 2009 (diff | hist) . . (+4,505) . . N Tarchive2amos (New page: tarchive2amos: utility for generating AMOS message files == Overview == The AMOS package uses a compact representation for the information exchange to and from the assembler. This repres...)
- 18:44, 8 July 2009 (diff | hist) . . (+1,012) . . N Ca2ace (New page: == Overview == Ca2ace can be used to convert assembler output in the Celera Assembler message format to the .ACE format (readable by consed). == Synopsis == ca2ace [options]-i <infil...) (current)
- 18:43, 8 July 2009 (diff | hist) . . (+1,003) . . N Amos2ace (New page: == Overview == Amos2ace can be used to convert assembler output in the AMOS message format to the .ACE format (readable by consed). == Synopsis == amos2ace [options] <infile1> <infil...) (current)
- 18:36, 8 July 2009 (diff | hist) . . (-78) . . AMOS Utilities (current)
- 18:36, 8 July 2009 (diff | hist) . . (+26) . . AMOS Utilities
- 18:33, 8 July 2009 (diff | hist) . . (+1,019) . . Wiki guide
- 18:18, 8 July 2009 (diff | hist) . . (+1) . . AMOS
- 18:17, 8 July 2009 (diff | hist) . . (+45) . . AMOS (→AMOS Development)
- 18:16, 8 July 2009 (diff | hist) . . (+1,145) . . N MUMmer (New page: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-mega...) (current)
- 18:15, 8 July 2009 (diff | hist) . . (-45) . . Programmer's guide (→AMOS messages and the Perl API)
- 18:14, 8 July 2009 (diff | hist) . . (-45) . . AMOS Getting Started (→Basic AMOS concepts)
- 18:12, 8 July 2009 (diff | hist) . . (-27) . . AMOS Getting Started
- 18:10, 8 July 2009 (diff | hist) . . (+4) . . Minimus
- 18:09, 8 July 2009 (diff | hist) . . (+10) . . Minimus
- 18:05, 8 July 2009 (diff | hist) . . (-164) . . AMOS Getting Started
- 18:03, 8 July 2009 (diff | hist) . . (+28) . . AMOSLib (current)
- 18:02, 8 July 2009 (diff | hist) . . (+24) . . AMOSLib
- 18:01, 8 July 2009 (diff | hist) . . (+26) . . AMOSLib
- 18:01, 8 July 2009 (diff | hist) . . (+2,963) . . N AMOSLib (New page: == Overview == The interface to the AMOS package is done through AMOS message files. This representation is described in detail here, and was inspired by the interchange format developed ...)
- 17:55, 8 July 2009 (diff | hist) . . (+75) . . AMOS Utilities
- 17:54, 8 July 2009 (diff | hist) . . (+2,488) . . N Select-reads (New page: == Overview == select-reads is a tool for selecting a subset of reads from a readbank, along with their fragments and library information. It can also automatically including the mates of...) (current)
- 17:51, 8 July 2009 (diff | hist) . . (+3,213) . . N AMOS Utilities (New page: Below is a short description of several useful tools or modules released with AMOS. Full documentation for some of these tools is still pending, however you can obtain the basic info by r...)
- 17:46, 8 July 2009 (diff | hist) . . (+7,008) . . N RunAmos (New page: == Overview == Most modern assembly programs (such as Celera Assembler or Arachne) consist of a series of modules, run in a pipeline fashion. The AMOS package includes a generic pipeline ...) (current)
- 17:43, 8 July 2009 (diff | hist) . . (+1) . . AMOS
- 17:41, 8 July 2009 (diff | hist) . . (+277) . . AMOS
- 17:41, 8 July 2009 (diff | hist) . . (-724) . . AMOS Documentation Project (current)
- 22:49, 7 July 2009 (diff | hist) . . (+81) . . AMOS
- 22:36, 7 July 2009 (diff | hist) . . (-2) . . AMOS
- 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)
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