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Old 11-19-2013, 01:39 PM   #6
rhall
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Location: San Francisco

Join Date: Aug 2012
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AHA is a separate scaffolding pipeline, if you have an illumina / 454 assembly <20,000 contigs <160 Mbase you can use PacBio long reads and AHA to scaffold and close gaps in the assembly.
You could also assembly with PacBioToCA then try scaffolding the resulting assembly with AHA in order to recover any of the sequence that was not in the PacBioToCA assembly due to illumina coverage bias.
Results from AHA should always be validated by resequencing of raw reads, to check for missassemblies.
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