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Introducing BBMerge: A paired-end read merger Brian Bushnell Bioinformatics 130 04-06-2020 03:12 AM
Merging paired ends fastq files with BBMerge bi_maniac Illumina/Solexa 19 11-04-2015 01:43 AM

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Old 02-15-2016, 12:07 AM   #1
Location: France

Join Date: Sep 2010
Posts: 27
Default bbmerge ratiomode ?

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
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Old 02-15-2016, 07:35 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

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.
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Old 02-16-2016, 10:58 AM   #3
Location: France

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Thanks Brian, thatīs more clear now !!!
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bbmap, bbmerge

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