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.

Hybrid error correction

Short read depth

We have used three short read depths (Raw, 118X and 100X) to correct long reads.

Long read depth

We have used subreads of 1-4 SMRT cells.

We arbitrary chose 1-4 SMRT cells: Three single SMRT cell: m120208_071634, m120228_192221, m120228_210845
Two SMRT cells: m120228_210845 + m120208_122534

Performance

Assembly

After read correction, PBcR can be used to de novo assembly by runCA or Mira3.