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Old 03-10-2015, 01:27 PM   #15
Junior Member
Location: Arlington, TX

Join Date: Mar 2013
Posts: 5
Default Optimal depth for read error correcting

Hi Brian and others,

I am wondering what depth you need and what depth is optimal (if the two differ) for proper read error correcting using BBMap or any other error correcting program. The Quake website mentioned >15x coverage but a quick round of Googling hasn't given me much more than that.

The reason I ask is because I have a couple lanes of MiSeq data (600 cycle PE sequencing), which individually total to about 3x coverage of my genome each. Therefore, a kmer based error correction wouldn't work well, even if I were to concatenate the two together. We do have an additional HiSeq lane (100bp PE) and a few GAII lanes (so 50-60x coverage total), so we have the option of concatenating all of the datasets together (though one GAII lane isn't paired-end). However, then we would have the separate the individual lanes back out, since we next plan to merge the MiSeq reads to create longer, 454-like reads.

Therefore, my second question is about what workflow would be best to accomplish this task? Are there some settings in or the like that would allow decent error correction with low coverage? Or alternatively, is there an easy way of separating data from different lanes if we were to concatenate a bunch together to give the coverage necessary to confidently correct? Thanks in advance for the help.
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