Skip to main content
. 2013 May 31;8(5):e65632. doi: 10.1371/journal.pone.0065632

Table 2. Comparison on 16 sets of programs and parameters using 100 bp paired-end simulated reads.

GPU CPU
6M 100 bp Paired-end reads, 1.2 Gbp bases. 500 bp insert size, 25 bp standard deviation. SOAP3-dp1 (1/4 SA) SOAP3-dp1 (1/2 SA) SOAP3-dp1 (Full SA) SOAP3-dp1 (Full SA, Binary) SOAP3-dp1 (Full SA, Succinct) SOAP3 Bowtie2 (Sensititve) Bowtie2 (Very-Sensititve) Bowtie2 (Very-fast) BWA2 SeqAlto SeqAlto (Fast alignement) CUSHAW2 GEM3 GEM3 (Fast Mapping: adaptive) GEM3 (Fast Mapping: 0)
Configuration CPU (thread: core i7-3930k) 4 4 4 4 4 4 4 4 4 4 4 4 4 4
GPU (device: GTX680) 1 1 1 1 0 0 0 0 0 0 0 0 0 0
Computational Total Elapsed sec. 132 137 162 111 112 132 966 1974 672 1154 495 379 1303 416 446 298
Resources Fold - 1.04 1.23 0.84 0.85 1.00 7.32 14.95 5.09 8.74 3.75 2.87 9.87 3.15 3.38 2.26
Loading Index4 sec. 32 46 74 74 74 74 38 38 38 53+1+1 96 96 40 40+1 40+1 40+1
Alignment5 sec. 100 91 88 37 38 58 928 1936 634 370+369+360 399 283 1263 199+176 238+167 90+167
Fold - 0.91 0.88 0.37 0.38 0.58 9.28 19.36 6.34 10.99 3.99 2.83 12.63 3.75 4.05 2.57
Avg. Memory GB 9.3 11.9 17.2 17.2 17.2 17.3 3.3 3.3 3.3 3.5 7 6.9 3.6 4.3 4.3 4.3
Peak Memory GB 9.7 12.5 18.1 18.1 18.1 19.2 3.5 3.5 3.5 4.8 7.2 7.2 3.6 4.3 4.3 4.3
Alignment Aligned # 11,999,827 11,870,740 11,999,763 11,999,936 11,998,226 11,998,804 12,000,000 11,995,872 11,999,975 11,999,763 11,999,484 11,995,422
Metrics Diff. - −129,087 −64 109 −1,601 −1,023 173 −3,955 148 −64 −343 −4,405
Properly Paired # 11,999,460 11,742,902 11,998,912 11,999,344 11,996,528 11,997,254 11,999,976 11,995,410 11,977,218 11,998,994 11,997,702 11,991,992
Diff. - −256,558 −548 −116 −2,932 −2,206 516 −4,050 −22,242 −466 −1,758 −7,468
Incorrectly Aligned # 40,561 138,655 143,012 141,373 147,764 85,297 95,672 99,243 99,243 56,514 61,642 61,887
Diff. - 98,094 102,451 100,812 107,203 44,736 55,111 58,682 150,036 15,953 21,081 21,326
Sensitivity6 % 99.66% 97.77% 98.81% 98.82% 98.75% 99.28% 99.20% 99.14% 99.17% 99.53% 99.48% 99.45%
Diff. - −1.89% −0.85% −0.84% −0.91% −0.38% −0.46% −0.52% −0.49% −0.13% −0.18% −0.21%
FDR7 % 0.34% 1.17% 1.19% 1.18% 1.23% 0.71% 0.80% 0.83% 0.83% 0.47% 0.51% 0.52%
Diff. - 0.83% 0.85% 0.84% 0.89% 0.37% 0.46% 0.49% 0.49% 0.13% 0.18% 0.18%
1

Alignment results by the three entries of SOAP3-dp (1/4 SA, 1/2 SA, Full SA) are identical.

2

The time consumption of BWA is calculated as “align left reads”+“align right reads”+“sampe”. The index loading times of “align right reads” and “sampe” modules are 1 second due to the reason that, index files were cached during “align left reads”. However, datasets larger than the host memory will flush the cache during alignment.

3

The alignment time consumption of GEM is calculated as “alignment”+“convert to SAM format”. The conversion module was run with 4 threads in consistent with the alignment module.

4

SOAP3-dp, SOAP3, SeqAlto and GEM aligners explicitly provide index loading time consumption. The index loading time for Bowtie2, CUSHAW2 and BWA are calculated by the total size of index, divided by 100 MB/s, which is the average network file system speed of the testing environment. The index loading time maybe underestimated while the time processing the index was not calculated.

5

The alignment times were explicitly provided by the aligners (include results processing and input/output time) or calculated by total elapsed time minus estimated index loading time.

6

Sensitivity is calculated as “Correctly aligned reads”/“All simulated reads”. The higher the better.

7

FDR is calculated as “Incorrectly aligned reads”/“All aligned reads”. The lower the better.