Table 2 StreamAligner performance (times reported in seconds)
From: StreamAligner: a streaming based sequence aligner on Apache Spark
Reference genome | Query genome | StreamAligner | SparkBWA | Speedup |
|---|---|---|---|---|
S_suis | 100 k | 18 | 81 | 4.5× |
chr1 | AML | 140 | 54 | 0.38× |
chr21 | AML | 147 | 44 | 0.3× |
hg19 | AML | 87 | 40 | 0.46× |
chr1 | BRL | 247 | 259 | 1.04× |
chr21 | BRL | 315 | 322 | 1.02× |
hg19 | BRL | 121 | 191 | 1.57× |
chr1 | ANL | 228 | 3189 | 13.98× |
chr21 | ANL | 1222 | 2403 | 1.96× |
hg19 | ANL | 337 | 3369 | 9.97× |
chr1 | ERR000589 | 532 | 1201 | 2.25× |
chr21 | ERR000589 | 178 | 407 | 2.28× |
hg19 | ERR000589 | 909 | 2202 | 2.42× |
chr1 | SRR015390 | 267 | 1093 | 4.09× |
chr21 | SRR015390 | 191 | 522 | 2.73× |
hg19 | SRR015390 | 568 | 2119 | 3.73× |
chr1 | SRR062634 | 779 | 1819 | 2.33× |
chr21 | SRR062634 | 624 | 1485 | 2.37× |
hg19 | SRR062634 | 1031 | 2321 | 2.25× |
chr1 | SRR642648 | 1449 | 2939 | 2.02× |
chr21 | SRR642648 | 1332 | 2500 | 1.87× |
hg19 | SRR642648 | 1892 | 3563 | 1.88× |