Arachne Main Page

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Under continuous development since 2000, the Arachne software package has evolved from the classic "overlap-layout-consensus" paradigm into a vast collection of different tools and modules, some to modify and manipulate assemblies, others to analyze and gather statistics or vizualize genomes. The current version of Arachne can be downloaded as source code.
Under continuous development since 2000, the Arachne software package has evolved from the classic "overlap-layout-consensus" paradigm into a vast collection of different tools and modules, some to modify and manipulate assemblies, others to analyze and gather statistics or vizualize genomes. The current version of Arachne can be downloaded as source code.
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This forum serves as a resource and to share information. It tells you how to install and run [[Arachne]], but it also talks at length about our experience assembling genomes, what algorithms we chose to implement and why, and what you can do to analyze and improve your draft genome. To participate in this wiki, please send mail to [mailto:arachne@broad.mit.edu arachne@broad.mit.edu] to ask for an account.
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To participate in this wiki, please send mail to [mailto:arachne@broad.mit.edu arachne@broad.mit.edu] to ask for an account.
== Downloads ==
== Downloads ==

Revision as of 20:06, 26 December 2007

frame:Spooky Spider


Arachne is the Whole Genome Shotgun Assembler developed at the Broad Institute.

Under continuous development since 2000, the Arachne software package has evolved from the classic "overlap-layout-consensus" paradigm into a vast collection of different tools and modules, some to modify and manipulate assemblies, others to analyze and gather statistics or vizualize genomes. The current version of Arachne can be downloaded as source code.

To participate in this wiki, please send mail to arachne@broad.mit.edu to ask for an account.

Contents

Downloads

  • Installation: how to download, install, and compile Arachne.

Using Arachne

  • Input: how to set up input files.
  • Running Arachne: from traces to the draft genome.
  • Output: how the output looks like, and how to translate it in a human readable format.
  • Analysis: how to examine your assembly.
  • Algorithms: you have your first assembly, now you want to make it better. Here, you might find out how.

Miscellaneous


External links

Personal tools