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  • merging assemblies with phrap

    Hi all,

    I recently finished assembly by mapping with MIRA, followed by Velvet de novo assembly of the missed reads. I am currently trying to merge both assemblies together using Phrap.

    My problem is, Phrap is taking a really long time with this re-assembly. I set my parameters as follows: penalty -9, minscore 100.

    My reference assembly consists of both contigs and scaffolds (with Ns). Do the Ns affect the run time for my merge? Is there anything I can do to make the re-assembly faster? Would it be better if I split the scaffolds at the Ns (maybe if > 10Ns are present)?

    Thanks in advance for your insight.

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