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

BMC Bioinformatics

Table 4 Results obtained by OverlapPER, PEAR, FLASH and COPE

Tool	Total merged pairs	% merged pairs	Mean length of merged sequences	Mean % identity	Mean mismatch	Mean gap opening	Run time (s)
OverlapPER	999,706	99.97%	391.69 ± 18.69	97.52% ± 0.70%	7.10 ± 2.66	2.62 ± 0.9	511. 26 ± 6.87
PEAR	995,648	99.56%	391. 19 ± 20.87	96.22% ± 1.31%	11.67 ± 4.87	3.04 ± 1.18	1363.37 ± 3.22
FLASH	326,686	32.67%	391.90 ± 19.54	97.38% ± 0.73%	7.55 ± 2.87	2.71 ± 0.97	49.93 ± 2.74
COPE	292,303	29. 23%	392.34 ± 19.46	97.45 ± 0.71	7.30 ± 2.77	2.70 ± 0.97	468.45 ± 0.81
BBMerge	201,842	20.18%	392.66 ± 19.25	97.49 ± 0.70	7.03 ± 2.69	2.83 ± 0.95	25. 23 ± 0.79

Parameters: minimum overlap of 10 bp and minimum identity of 90%. Mean identity, mismatch and gap openings are shown in comparison to the reference genome
A total of 1,000,000 simulated reads were used as input for the evaluated tools. The results are shown regarding the absolute number of total merged pairs of sequences, the percentage of merged pairs, the mean length of the resulting merged sequences, the mean percentage identity when aligning the resulting sequences to the reference genome, the mean total of mismatch and gap openings resulted from the alignment and finally the mean run time took for each tool

ISSN: 1471-2105