Table 2. Aligner run times in wall-clock hours.
Each aligner was tested by aligning all 67 groups of simulated Illumina reads in single and paired-end mode. The maximum number of threads utilizable by each aligner were used in testing.
| Aligner | # Threads
Utilizable (of 24) |
PE Time to
align |
SE Time to
align |
|---|---|---|---|
| BWA | 24 | 0.28 | 0.08 |
| Bfast | 24 | 19.79 | 7.01 |
| Smalt | 8 | 6.44 | 8.25 |
| Stampy | 1 | 6.28 | 3.50 |
| Mosaik | 24 | 2.64 | 1.56 |
| CLC | 24 | 1.41 | 0.88 |
| CLCBeta | 24 | 0.67 | 0.60 |
| Novoalign | 24 | 0.11 | 0.04 |
| Omixon | 24 | 4.83 | 1.26 |
| Bowtie2 | 24 | 0.30 | 0.11 |
| Nextgene | 24 | NA | NA |