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Tools
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Coral, error correction that uses Illumina to correct 454:

  http://www.cs.helsinki.fi/u/lmsalmel/coral/

Kraken, de novo adapter discovery:

  http://biorxiv.org/content/early/2013/11/14/000422

SSPACE for scaffolding:

  http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/

BESST for scaffolding:

  https://github.com/ksahlin/BESST