Consensus BaseSearch for each position for forward and reverse reads for a base:
If different bases are found for forward and reverse reads, unite forward and reverse and repeat algorithm above on this single list. Finally, do an ambiguity check:
Consensus Base QualityConsensus gaps have always quality 0. If consensus is not a gap, use MIRA-Like consensus quality calculation: Best quality for a base in a direction makes basic rate = 100% add to this: 10% of next best base quality. Same procedure for other direction (if available), then add both qualities In general, the values are almost the same (mostly a tad higher) as with the more complicated (and time consuming) old variant. Cap at 90. Example: + A 30 -> 30 \ + A 20 -> 2 \ + A 20 / = 32 \ + A 20 / \ > = 60 - A 26 -> 26 \ / - A 20 -> 2 > = 28 / - A 15 / (+ = forward. - = reverse)
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