Program | Wall time | CPU time | Memory |
|---|
FAAST 1.0 | 6m38s | 51m26s | 348 Mb |
SSAHA2 2.5.3 | 4m48s | 4m48s | 271 Mb |
BLAST 2.2.21 | 28m30s | 46m09s | 37.8 Mb |
- Resources exhausted by FAAST, SSAHA2 and BLAST in alignment of 221,245 454 reads (45.8 Mbp in total) against a database of 11,178 sequences (65.3 Mbp in total). The test was performed on a 64-bit Linux machine with an 'Intel Core i7 920' processor, HT enabled. FAAST was executed with default parameters, thus indexing 11-mer nucleotides running in 8 threads and reporting 10 results per query. SSAHA2 was executed with the parameters '-kmer 11 -skip 2 -best 10 -seeds 2' and BLAST with '-v10 -b10 -a8' also indexing 11-mer nucleotides and reporting top 10 hits. The SSAHA2 and BLAST times do not include times for building the database (ssaha2Build and formatdb).
