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Fig. 3 | BMC Bioinformatics

Fig. 3

From: PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly

Fig. 3

Merging process for paired-end reads. a OverlapPER script first finds a seed (a short sequence in one of the reads represented in bold) (b) The reads are positioned according to the seed found and the total overlap is determined. c The total overlap is analyzed. If there is a hit in the alignment, the identity score is incremented. If a base is aligned to a gap, the identity score is incremented. In case of a mismatch in the alignment, if the next 5 bases (tolerance) are identical, the mismatch score is incremented, otherwise a gap insertion is repeated 4 times until the next 5 bases are identical. Nucleotides in bold represent a hit in the alignment

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