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<big>'''IMAGE is now published on Genome Biology'''</big>
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== News ==
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[http://genomebiology.com/2010/11/4/R41 Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps]
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== Getting started ==
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'''IMAGE is now published on Genome Biology!'''
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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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[http://genomebiology.com/2010/11/4/R41 "Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps"]
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* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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== Methods ==
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* [[How to run IMAGE]]
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* [[IMAGE protocols]]
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* [[IMAGE Faqs]]
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IMAGE is in constant development and probably been used elsewhere other than its intended purposes ; Please contact [mailto:jit@sanger.ac.uk Jason] for any discussions and bugs.
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== What is IMAGE? ==
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IMAGE stands for Iterative Mapping and Assembly for Gap Elimination. It is a software designed to close gaps in any draft assembly using Illumina paired end reads. IMAGE is best described in several stages: aligning of Illumina reads at contig ends; local assembly of reads into new contigs; reference contigs are extended or merged; iterating the whole process to extend and merge more contigs.
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[[File:Figure1.jpg]]
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IMAGE has been used in the Parasites Genomics group at the Wellcome Trust Sanger Institute, and is in the process of implementing into the Ensembl pipeline to improve reference genome sequence.
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== Download IMAGE ==
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IMAGE available [https://sourceforge.net/projects/image2/files/ here]
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== Changes ==
 +
* 03.11.13 v2.4.1 uploaded
 +
  - small bug fix on restartIMAGE.pl thanks to Pallavi Singh
 +
 
 +
* 30.10.13 v2.4 uploaded
 +
  - small bug fix on restartIMAGE.pl thanks to Binshuang Li from Rochester
 +
  - added new stable codes on how to handle very small contigs (300~500bp) in scaffolds.
 +
 
 +
* 25.04.12 two small bug fixed
 +
  - thanks to Roy Chaudhuri from Cambridge
 +
 
 +
* 10.12.11 various bug fixed
 +
    - -vel_ins_len option is now working
 +
 
 +
 
 +
* 10.11.11 various bug fixes
 +
    - The partitioned function is now default.
 +
 
 +
* 09.11.11 various bug fixes
 +
    - various scripts now available for clearer interpretations of results
 +
    - A partitioned function that lets image to run only on 10% of original data,
 +
      highly recommended if the genome in question is reasonably large
 +
 
 +
* 24.10.11 a "tidier" version of image is released
 +
    - default mapper becomes smalt, bwa and ssaha obsoleted
 +
    - example should be run in less than 5 minutes.
 +
 
 +
* 12.05.10 version2.1 released (bug fixes thanks to report from Monica Britton)
 +
* Fixed the inconsistencies between the ssaha2/bwa components of IMAGE accepting .fastq.gz or .fastq (Thanks to Brian)
 +
* Fixed the parsing error when there was no contigs produced by velvet (Thanks to Zen Lu)

Revision as of 00:24, 3 November 2013

Contents

News

IMAGE is now published on Genome Biology!

"Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps"


Methods

IMAGE is in constant development and probably been used elsewhere other than its intended purposes ; Please contact Jason for any discussions and bugs.


What is IMAGE?

IMAGE stands for Iterative Mapping and Assembly for Gap Elimination. It is a software designed to close gaps in any draft assembly using Illumina paired end reads. IMAGE is best described in several stages: aligning of Illumina reads at contig ends; local assembly of reads into new contigs; reference contigs are extended or merged; iterating the whole process to extend and merge more contigs.


File:Figure1.jpg


IMAGE has been used in the Parasites Genomics group at the Wellcome Trust Sanger Institute, and is in the process of implementing into the Ensembl pipeline to improve reference genome sequence.

Download IMAGE

IMAGE available here


Changes

  • 03.11.13 v2.4.1 uploaded
  - small bug fix on restartIMAGE.pl thanks to Pallavi Singh
  • 30.10.13 v2.4 uploaded
  - small bug fix on restartIMAGE.pl thanks to Binshuang Li from Rochester
  - added new stable codes on how to handle very small contigs (300~500bp) in scaffolds. 
  • 25.04.12 two small bug fixed
  - thanks to Roy Chaudhuri from Cambridge
  • 10.12.11 various bug fixed
   - -vel_ins_len option is now working


  • 10.11.11 various bug fixes
   - The partitioned function is now default.
  • 09.11.11 various bug fixes
    - various scripts now available for clearer interpretations of results
    - A partitioned function that lets image to run only on 10% of original data, 
      highly recommended if the genome in question is reasonably large
  • 24.10.11 a "tidier" version of image is released
    - default mapper becomes smalt, bwa and ssaha obsoleted
    - example should be run in less than 5 minutes.
  • 12.05.10 version2.1 released (bug fixes thanks to report from Monica Britton)
  • Fixed the inconsistencies between the ssaha2/bwa components of IMAGE accepting .fastq.gz or .fastq (Thanks to Brian)
  • Fixed the parsing error when there was no contigs produced by velvet (Thanks to Zen Lu)
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