Table 3 The output statistics and derived statistics from running five pairs of NGS datasets through the SA_Run2Run workflow.
From: SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data
NGS datasets | Ecoli_I4M_R1 | Ecoli_I4M_R2 | Ecoli_454_500K | ECT_R1 | ECT_rerun_R1 | ECT_R2 | ECT_rerun_R2 | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Â | Run1 | Run2 | Run1 | Run2 | Run1 | Run2 | Run1 | Run2 | Run1 | Run2 |
Output statistics | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
Total number of raw reads in the run | 2,000,000 | 2,000,000 | 2,000,000 | 2,000,000 | 250,000 | 250,000 | 7,575,822 | 7,064,035 | 7,575,822 | 7,064,035 |
Total number of cleaned reads in the run | 1,968,732 | 1,997,550 | 1,999,692 | 1,999,283 | 231,123 | 231,245 | 7,538,930 | 7,046,481 | 7,542,743 | 7,046,396 |
Number of unique reads in the run (after removing identical redundant reads) | 1,487,552 | 1,482,834 | 1,450,704 | 1,405,779 | 224,217 | 224,537 | 7,114,791 | 6,702,601 | 7,242,351 | 6,839,442 |
Number of unique reads in the run (after removing identical & inclusive redundant reads) | 1,487,552 | 1,482,834 | 1,450,704 | 1,405,779 | 221,379 | 221,622 | 6,885,175 | 6,407,251 | 6,945,743 | 6,546,440 |
Total number of overlapping reads in the run | 712,022 | 730,780 | 810,225 | 834,999 | 18,304 | 18,321 | 950,696 | 941,648 | 807,790 | 770,963 |
Number of unique overlapping reads in the run | 360,898 | 360,898 | 403,927 | 403,927 | 15,786 | 15,786 | 621,978 | 617,458 | 537,199 | 530,419 |
Number of unique overlapping reads from both runs | 360,898 | 403,927 | 15,786 | 625,044 | 538,561 | |||||
Derived satistics | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
File size after preprocessing | 266MB | 266MB | 266MB | 266MB | 216MB | 216MB | 2.6GB | 2.4GB | 2.5GB | 2.4GB |
Number of redundant cleaned reads in the run | 481,180 | 514,716 | 548,988 | 593,504 | 9,744 | 9,623 | 653,755 | 639,230 | 597,000 | 499,956 |
Redundancy rate within the run | 32.3% | 34.7% | 37.8% | 42.2% | 4.4% | 4.3% | 9.5% | 10.0% | 8.6% | 7.6% |
Total number of non-overlapping reads in the run | 1,256,710 | 1,266,770 | 1,189,467 | 1,164,284 | 212,819 | 212,924 | 6,588,234 | 6,104,833 | 6,734,953 | 6,275,433 |
Number of unique non-overlapping reads in the run | 1,126,654 | 1,121,936 | 1,046,777 | 1,001,852 | 205,593 | 205,836 | 6,263,197 | 5,789,793 | 6,408,544 | 6,016,021 |
Number of redundant non-overlapping reads in the run | 130,056 | 144,834 | 142,690 | 162,432 | 7,226 | 7,088 | 325,037 | 315,040 | 326,409 | 259,412 |
Redundancy of non-overlapping reads in the run | 11.5% | 12.9% | 13.6% | 16.2% | 3.5% | 3.4% | 5.2% | 5.4% | 5.1% | 4.3% |
Number of redundant overlapping reads in the run | 351,124 | 369,882 | 406,298 | 431,072 | 2,518 | 2,535 | 328,718 | 324,190 | 270,591 | 240,544 |
Redundancy of overlapping reads in the run | 97.3% | 102.5% | 100.6% | 106.7% | 16.0% | 16.1% | 52.9% | 52.5% | 50.4% | 45.3% |
Total overlapping reads/total cleaned reads (each run) | 36.2% | 36.6% | 40.5% | 41.8% | 7.9% | 7.9% | 12.6% | 13.4% | 10.7% | 10.9% |
Total overlapping reads/total cleaned reads (both runs) | 36.4% | 41.1% | 7.9% | 13.0% | 10.8% | |||||
Total runtime (min) | 13.3 | 13.0 | 8.2 | 106.3 | 110.8 | |||||