Arachne Main Page

From ArachneWiki

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

• Setup
• Input
• Running Arachne
• Output
• Looking at Assemblies
• Improving Assemblies
• Independent Modules

Downloads

• Nightly Build: The current state of Arachne - updated within the last 24 hours.
• Sample Projects: Ready-made examples of Arachne input.

Public tools

• Online help: crdhelp@broadinstitute.org

Miscellaneous

• Arachne's lore

External links

• Genome assembly
• Shotgun sequencing
• Broad Institute

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 (2009), R88.