Programs | Index time (min) | Alignment time (min) | Reads aligned (%) |
|---|
SOAP2 (2.20) | 89.50 | 15.4 | 75.96 |
Bowtie (0.12.3) | 192.00 | 21.2 | 75.71 |
BWA (0.5.8 C) | 101.50 | 26.4 | 76.12 |
Novoalign (2.07.00) | 4.02 | 62.9 | 74.61 |
- Index is built on the human genome 18 for each aligner. 7.4 million single-end reads are then mapped onto the human genome 18. The read length is 68 bp. At most two mismatches are allowed in all programs, and one alignment is randomly reported for each read. The CPU time in minutes on dual quad-core 2.66Ghz Xeon E5430 processor for index building and alignment processing, as well as percent of mapped reads, are shown in this table.
