Arachne Main Page

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[[Arachne]] is the [[w:Shotgun sequencing|Whole Genome Shotgun]] Assembler developed at the [[w:Broad Institute|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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[[ArachneWiki:About|The ArachneWiki]] is Arachne's online home. To participate in this wiki, please send mail to [mailto:arachne-dev@broad.mit.edu arachne-dev@broad.mit.edu] to ask for an account.
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== Quick Links ==
== Quick Links ==
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=== Downloads ===
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=== Arachne Reference ===
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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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* [[Setup]]
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* [[Stable Build]]: The latest stable, trustworthy version of Arachne.
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* [[Sample Project]]s: ready-made examples of Arachne input.
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=== Public tools ===
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* [http://bugzilla.broad.mit.edu/arachne/ Bugzilla]: Bug tracking system
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* [mailto:arachne@broad.mit.edu arachne@broad.mit.edu]: Mailing list
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=== Reference ===
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* [[Setup]]: how to download, install, and compile Arachne.
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* [[Input]]
* [[Input]]
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* [[Running Arachne]]: from traces to the draft genome.
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* [[Running Arachne]]
* [[Output]]
* [[Output]]
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* [[Analysis]]: how to examine your assembly.
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* [[Looking at Assemblies]]
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* [[Restricted:Algorithms|Algorithms]]: For improving assemblies.
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* [[Improving Assemblies]]
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* [[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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== External links ==
== External links ==
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* [[w:DNA sequencing|DNA sequencing]]
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* [[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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