Arachne Main Page

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__NOTOC__
__NOTOC__
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Welcome to [[ArachneWiki:About|the ArachneWiki]]! This is the online home of [[Arachne]], the [[Whole Genome Shotgun Assembly|Whole Genome Shotgun Assembler]] developed at the [http://www.broad.mit.edu/ Broad Institute].
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[[Arachne Main Page|ARACHNE]] is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.
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== Quick Links ==
== Quick Links ==
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=== Downloads ===
 
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* [ftp://ftp.broad.mit.edu/pub/wga/Arachne_nightly/ Nightly Build]: The current state of Arachne - updated within the last 24 hours.
 
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* [ftp://ftp.broad.mit.edu/pub/wga/Arachne_stable/ Stable Build]: The latest stable, trustworthy version of Arachne.
 
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* [ftp://ftp.broad.mit.edu/pub/wga/sample_projects/ Sample Projects]: Ready-made examples of Arachne input.
 
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=== Public tools ===
 
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* [[Bug tracking system]]: [https://www.broad.mit.edu/wga/bugzilla/ Bugzilla]
 
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* [[Mailing list]]: [mailto:arachne@broad.mit.edu arachne@broad.mit.edu] (e-mail the list to request a subscription)
 
=== Arachne Reference ===
=== Arachne Reference ===
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* [[Improving Assemblies]]
* [[Improving Assemblies]]
* [[Independent Modules]]
* [[Independent Modules]]
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=== Downloads ===
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* [ftp://ftp.broadinstitute.org/pub/crd/nightly/arachne/ Nightly Build]: The current state of Arachne - updated within the last 24 hours.
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* [ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/sample_projects.tar.gz Sample Projects]: Ready-made examples of Arachne input.
=== Miscellaneous ===
=== Miscellaneous ===
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* [[ArachneWiki:About|About ArachneWiki]]
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* Arachne's [[lore]]
* Arachne's [[lore]]
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* [[w:Genome assembly|Genome assembly]]
* [[w:Genome assembly|Genome assembly]]
* [[w:Shotgun sequencing|Shotgun sequencing]]
* [[w:Shotgun sequencing|Shotgun sequencing]]
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* [http://www.broad.mit.edu/ Broad Institute]
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* [http://www.broadinstitute.org/ Broad Institute]
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== Publications ==
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Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. January, 2002. ''[http://www.ncbi.nlm.nih.gov/pubmed/11779843 ARACHNE: a whole-genome shotgun assembler. Genome Research]'' 12: 177 - 189.
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Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. January, 2003. ''[http://www.ncbi.nlm.nih.gov/pubmed/12529310 Whole-genome sequence assembly for mammalian genomes: Arachne 2]. Genome Research'' 13: 91 - 96.
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Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB: August, 2009.
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''[http://genomebiology.com/2009/10/8/R88 Assisted assembly: how to improve a de novo genome assembly by using related species]. Genome Biology'' 10: R88.

Current revision

ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.


Quick Links

Arachne Reference

Downloads

Miscellaneous

External links

Publications

Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. January, 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12: 177 - 189.

Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. January, 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Research 13: 91 - 96.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB: August, 2009. Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biology 10: R88.

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