Benchmarking Data
Listed below is representative benchmarking data created by using a computer with specifications similar to those listed on our technical requirements page for the applicable experiment.
SeqMan NGen Reference Guided Assembly Benchmarks
Data Set |
Reference Sequence |
Genome Size (Mbp) |
Sequence Technology |
Number of Reads (M) |
Number of Bases (Mbp) |
Coverage |
Assembly Time** (H:M:S)
|
| Human Genome* |
Hg19+dbSNP |
3,101 |
Illumina |
3,521 |
127,000 |
35X |
22:23:00 |
| Human Genome* |
Hg19+dbSNP |
3,101 |
Roche 454 |
74 |
19,700 |
6X |
06:13:56 |
| Human Exome* |
|
3,101 |
Illumina |
166 |
12,600 |
148X |
03:14:04 |
| Rice Genome* |
|
382 |
Illumina |
272 |
8,900 |
20X |
02:04:16 |
| Yeast Genome |
1999 SGD |
12 |
Roche 454 |
1 |
300 |
21X |
00:03:53 |
| K-12 E. coli Genome* |
DH 10B |
5 |
Illumina |
4 |
150 |
30X |
00:01:10 |
| K-12 E. coli Genome |
DH 10B |
5 |
Ion Torrent |
1 |
148 |
19X |
00:01:06 |
| "Deep" K-12 E. coli Genome* |
MG 1655 |
5 |
Illumina |
45 |
4,700 |
996X |
00:29:38 |
SeqMan NGen de novo Assembly Benchmarks
Data Set |
Sequence Technology |
Number of Reads (K) |
Number of Bases (M) |
Coverage |
ContigN50 (Kbp) |
Assembly Time** (H:M:S)
|
| K-12 E. coli Genome* |
Roche 454 |
385 |
69 |
18X |
56 |
00:22:34 |
| K-12 E. coli Genome* |
Illumina |
1,150 |
115 |
50X |
44 |
00:38:18 |
| Rodent Transcriptome* |
Roche 454 |
1,000 |
570 |
NA |
NA |
04:48:00 |
*Data sets for these projects were obtained from NCBI's Short Read Archive.
**Assembly times were calculated using a computer with a 4-Disk RAID-0. Assemblies run with a 2-Disk RAID-0 were approximately 20-40% slower for moderate-sized data sets, such as mid-sized genomes.
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