Table 1 Comparison of PIPEBAR to SeqTrace and Geneious regarding to the total of barcodes produced at the end of the pipeline execution for the 3 datasets, mean similarity percentage of all the resulting barcodes to its respective Bold reference sequence, the time spent for each pipeline counting from sequences trimming to the final results, total sum of mismatches and gap openings by applying Blastn [44] against the FASTA of ab1 files retrieved from Bold
From: PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly
| Â | Dataset 1 (841 plant marker genes) | Dataset 2 (558 animal marker genes) | Dataset 3 (490 fungi marker gene) | ||||||
|---|---|---|---|---|---|---|---|---|---|
PIPEBAR | SeqTrace | Geneious | PIPEBAR | SeqTrace | Geneious | PIPEBAR | SeqTrace | Geneious | |
Resulting barcodes | 830 | 841 | 829 | 557 | 558 | 555 | 448 | 487 | 438 |
Mean % identity | 99.88 ± 0.17 | 99.68 ± 0.41 | 99.92 ± 0. 12 | 99.88 ± 0.16 | 99.56 ± 0.44 | 99.91 ± 0.11 | 99.67 ± 0.52 | 98.79 ± 1.73 | 99.73 ± 0.43 |
Mean % length | 557.51 ± 49.2 | 575 ± 161. 6 | 549.81 ± 42.5 | 637.82 ± 28.98 | 638.54 ± 29.36 | 638.45 ± 28.85 | 618.50 ± 48.01 | 585.52 ± 81.53 | 619 ± 45.3 |
Run time (s) | 25 | 367 | 197 | 21 | 296 | 98 | 17 | 231 | 160 |
Mismatches | 372 | 941 | 294 | 140 | 383 | 96 | 267 | 930 | 224 |
Gap openings | 91 | 266 | 41 | 17 | 115 | 12 | 82 | 341 | 72 |