bbmerge ratiomode ?

[danova]

Hi,
bbmerge seems to use by default the ratiomode as follows:

ratiomode=t Newer algorithm. Slower, but higher merge rate.
Much better for long overlaps and high error rates.
maxratio=0.09 Max error rate; higher increases merge rate.

I have a couple of question. Is there any documentation on how this works ??? Also maxratio=0.09 means an error rate of 9% per base ??? I guess this is for pacbio reads ?? short illumina reads should still work with a maxratio of 0.01 ?

thanks for the update
david

[Brian Bushnell]

Hi David,

BBMerge is designed exclusively for Illumina reads. PacBio are not paired anyway so there's no point in using it there. It could theoretically be used with Ion Torrent, but I have never tested it and it is not designed to be robust against indel-type sequencing errors.

BBMerge is documented in bbmap/docs/guides/BBMergeGuide.txt. However, that does not really describe the algorithm. I'm working on a BBMerge paper which will describe the algorithm; should be out in a couple months.

maxratio=0.09 actually indicates a 9% rate of disagreement between read 1 and read 2, which is closer to a 4.5% error rate. Illumina short reads may work with maxratio=0.01 but the merge rate would be lower. Remember, this is only for the overlapping part of the read, which is toward the end in the lowest-quality area.

[danova]

Thanks Brian, that´s more clear now !!!