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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
danova
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Default bbmerge ratiomode ?

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
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Old 02-15-2016, 07:35 PM   #2
Brian Bushnell
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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
danova
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Thanks Brian, thatīs more clear now !!!
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