Table 2 Execution times of commonly used software: comparison of XplorSeq with command line implementation
| Â | Execution Time (sec.)1 | Â | Â | |||
|---|---|---|---|---|---|---|
| Â | System A2 | System B3 | Â | Â | ||
Program | XplorSeq4 | Command Line | XplorSeq4 | Command Line | Task | Sequence Data |
phred | 50.5 (5.3)1 | 51.0 (2.9)1 | 23.3 (0.8)1 | 19.3 (0.5)1 | Basecall | 768 .esd files. |
phrap | 167.0 (2.4) | 153.3 (0.8) | 30.5 (1.2) | 28.8 (1.5) | Contig | 384 pairs of reads. |
blastall | 368.0 (2.4) | 345.3 (0.8) | 228.5 (1.2) | 221.3 (2.4) | Local blast | 24 1585-mers |
XplorSeq | 69.0 (8.1) | na | 21.2 (0.4) | na | Import fasta | 250,000 1585-mers |
XplorSeq | 130.8 (10.8) | na | 12.2 (0.4) | na | Open XplorSeq file | 250,000 1585-mers |
XplorSeq | 160.8 (14.4) | na | 11.7 (0.5) | na | Save XplorSeq file | 250,000 1585-mers |
XplorSeq | 60.5 (0.8) | na | 46.3 (1.4) | na | Import fasta | 1,000,000 25-mers |
XplorSeq | 216.3 (11.2) | na | 28.0 (0.6) | na | Open XplorSeq file | 1,000,000 25-mers |
XplorSeq | 34.3 (3.8) | na | 16.5 (0.5) | na | Save XplorSeq file | 1,000,000 25-mers |