As described in the paper Hybrid error correction, second-generation data can be used to correct PacBio reads and then perform de novo assembly using PacBio corrected reads (PBcR). Here, we discuss the effects of depths on (1) hybrid error correction and (2) assembly.
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We have used three short read depths (Raw, 118X and 100X) to correct long reads.
We have used subreads of 1-4 SMRT cells. We arbitrary chose 1-4 SMRT cells: One SMRT cell: m120208_071634 Two SMRT cells:
After read correction, PBcR can be used to de novo assembly by runCA or Mira3.