Mapping Times and Accuracies
random10k test set - randomly generated "genome" of just 10k. Reads are one 25-mer at each
position. Percentage numbers in table are the proportion of reads that were mapped by the various
programs using the given settings. All programs completed this short test quickly. This test
highlights splat's capability of handling single base insertions and deletions as well as the up to
two substitutions per read that most of the programs handle.
sub ins del splat splat soap soap soap maq eland eland bowtie
per per per default maxGap=0 default -g 1 -g 1 default default --multi default
read read read -s 6
----------------------------------------------------------------------------------------------
0 0 0 100.00% 100.00% 100.00% 100.00% 100.00% 99.86% 100.00% 100.00% 100.00%
1 0 0 100.00% 100.00% 100.00% 100.00% 100.00% 99.86% 100.00% 100.00% 100.00%
2 0 0 100.00% 100.00% 96.37% 96.37% 97.70% 99.88% 100.00% 100.00% 100.00%
0 1 0 100.00% 27.08% 28.04% 91.10% 90.97% 22.69% 22.69% 22.69% 22.69%
1 1 0 100.00% 19.85% 17.45% 17.52% 17.47% 15.61% 15.61% 15.61% 15.61%
0 0 1 100.00% 31.90% 22.69% 82.20% 82.92% 27.94% 28.04% 28.04% 28.04%
1 0 1 100.00% 21.73% 15.61% 19.60% 19.60% 17.37% 17.45% 17.45% 17.45%
hardSim22 test set - chromosome 22 with simulated errors mapped back to chromosome 22.
This was generated with the maq simulate command with a relatively high error rate of about
2 errors per read on average. 10% of errors are indels. Splat maps significantly more reads
than the others. The run-times are minutes:seconds.
splat soap soap maq eland eland bowtie
default -g 1 default default --multi=100 default
reads time mapped time mapped time mapped time mapped time mapped time mapped time mapped
----------------------------------------------------------------------------------------------------------------
1 0:11 100.00% 0:09 100.00% 0:08 100.00% 0:55 100.00% 0:22 100.00% 0:25 100.00% 0:02 100.00%
10 0:11 90.00% 0:08 80.00% 0:09 90.00% 0:55 80.00% 0:22 70.00% 0:24 80.00% 0:02 80.00%
100 0:13 79.00% 0:08 71.00% 0:08 72.00% 0:54 74.00% 0:21 40.00% 0:24 70.00% 0:02 71.00%
1000 0:11 78.20% 0:08 71.50% 0:10 72.30% 1:13 73.20% 0:22 46.30% 0:23 70.60% 0:02 71.80%
10000 0:16 75.84% 0:13 69.68% 0:14 70.99% 1:32 72.29% 0:23 43.67% 0:23 68.96% 0:03 70.13%
100000 0:33 76.34% 0:43 70.07% 0:58 71.66% 2:02 72.49% 0:31 44.21% 0:30 68.65% 0:11 70.54%
1000000 3:15 76.33% 5:59 70.07% 8:49 71.69% 6:36 72.53% 1:46 44.14% 1:46 61.83% 1:24 70.54%
tenMegVs22 test set - 10,000,000 chr22 reads with simulated errors averaging one per read,
10% of errors are indels.
splat soap soap maq eland eland bowtie
default default -g 1 default default --multi=100 default
reads time mapped time mapped time mapped time mapped time mapped time mapped time mapped
----------------------------------------------------------------------------------------------------------------
10000000 39:58 95.49% 43:16 91.58% 49:52 93.27% 62:09 92.78% 13:11 75.28% 13:49 90.24% 8:47 91.91%
14vs22 test set - part of chromosome 14 that is a duplicon of chr22 repeat masked, and
non-masked parts shredded into non-overlapping 25-mers and mapped to chr22 (10252 reads)
splat soap soap maq eland eland bowtie
default default -g 1 default default --multi=100 default
reads time mapped time mapped time mapped time mapped time mapped time mapped time mapped
---------------------------------------------------------------------------------------------------------------
10252 0:14 96.20% 0:09 95.77% 0:09 96.03% 1:23 95.79% 0:18 90.17% 0:21 95.71 0:02 95.80%
bigChrom test set - 1 million simulated reads (same as in first test set) with simulated
error averaging 2 per read, 10% of errors are indels, against bigger and bigger sets of chromosomes.
splat soap soap maq eland eland bowtie
default default -g 1 default default --multi=100 default
size chroms time mapped time mapped time mapped time mapped time mapped time mapped time mapped
--------------------------------------------------------------------------------------------------------------------
35M 22 3:15 76.33% 5:59 70.07% 8:49 71.69% 6:36 72.53% 1:46 44.14% 1:46 61.83% 1:24 70.54%
69M 21,22 4:20 76.70% 11:38 70.04% 14:48 72.07% 12:27 72.94% 2:31 43.75% 2:20 69.60% 1:47 70.74%
142M 18,21,22 6.38 77.20% 20:10 71.01% 26:20 72.57% 21.42 73.50% 4:56 43.17% 4:33 69.72% 2:13 70.60%
273M 2,22 10:24 77.80% 34:19 71.64% 53.16 73.15% 34.05 74.14% 6:35 42.17% 7:21 69.95% 2:20 70.09%
3080M all n/a n/a n/a n/a n/a n/a 4:26 69.77%
Database and Index Times and Sizes
Some of the programs need either a sequence database, or a sequence index to be built.
This table looks at the time and build sizes for these for chromosome 22, some data sets
that are roughly 2x, 4x, and 8x as large as chromosome 22, and for the entire human genome.
Splat spends significantly longer on this index/database building phase than the other
programs (nothing comes for free) but still, this only needs to be done once per genome.
DNA splat soap maq eland bowtie
size time size time size time size time size time size
------------------------------------------------------------------------
35M 0:59 953M 0 0 0:02 25M 0:01 24M 1:45 37M
69M 1:39 1820M 0 0 0:04 48M 0:02 47M 3:36 66M
143M 3:30 3688M 0 0 0:07 86M 0:03 83M 8:21 127M
272M 7:16 6901M 0 0 0:12 146M 0:05 140M 18:30 233M
2858M 80:00* 72000M* 0 0 2:05 1554M 0:40 1470M
* Estimated - need machine with more RAM than we have (about the same amount of ram as the file size)
to make or use the index. Currently this restricts splat to be run one chromosome at a time on most
machines.