Hi guys,
I am writing an tool for amplicon sequencing, which needs to condense reads mapping to the same position. At the moment, I just take the most frequent read, which is obviously far from perfect, especially in low quality or low coverage situations.
While it is easy to calculate the consensus of the base string and to approximate the quality, the CIGAR string is much harder. Does anyone has an algorithm or even source code to do this?
Best
Flo
I am writing an tool for amplicon sequencing, which needs to condense reads mapping to the same position. At the moment, I just take the most frequent read, which is obviously far from perfect, especially in low quality or low coverage situations.
While it is easy to calculate the consensus of the base string and to approximate the quality, the CIGAR string is much harder. Does anyone has an algorithm or even source code to do this?
Best
Flo
Comment