SeqMan NGen- Next-Gen Sequence Assembly Software, De Novo Sequence Assembly Software, Reference-Guided Alignment Software  

 

Benchmarking Data

Listed below is representative benchmarking data for both reference-guided and de novo assemblies, 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
Sequence Technology
Reference Sequence
Genome Size (Mbp)
Number of Reads (M)
Number of Bases (Mbp)
Read Length (bp) Coverage

Assembly Time**

Human Genome* Illumina Hg19+dbSNP 3,101 1,499 14,990 100 48X 13 Hrs.
8 Human Exomes* (multiplex) Illumina

Hg19+dbSNP

27 1,268 12,047 76 446X 14 Hrs
Human Exome*
Illumina
27
163
12,390
76
459X
2 Hrs.
Ion AmpliSeq™ Cancer Panel (3 multiplexed data
sets) Data provided by Ion Torrent.
Ion Torrent
3,101
3
99
85 500X
24 Min.
Fluidigm® Access Array System (2 multiplexed data
sets) Data provided by Pacific Biosciences.
Pacific Biosciences Fluidigm human amplicons 0.1 < 1 7 180 500X 1 Min.
Rice Genome* Illumina IRGSP build 4 + dbSNP 382 272 8,708 32 23X 1.5 Hrs.
Arabidopsis Genome* Illumina TAIR10 120 67 5,000 75 42X 1 Hr.
Aspergillus Genome* Roche 454
ASM265v1
29
2
1,055
450 36X
38 Min
K-12 E. coli Genome*
Illumina
MG1655
5
2.5
250
100
50X
1 Min.
"Deep" K-12 E. coli Genome*
Illumina
MG1655
5
45
4,539
100
908X
28 Min.
K-12 E. coli Genome (merge pair data) Data provided by Ion Torrent.
Merged pair data consists of overlapping forward and reverse reads.
SeqMan NGen aligns these reads and merges them into a single consensus.
Ion Torrent
DH10B

5

3 M
387
115
77X
7 Min.
K-12 E. coli Genome*
Roche 454
MG1655
5
1.5 M
606
400
121X
3 Min.
K-12 E. coli
GenomeSOLiD data is imported as a BAM file.
SOLiD
DH10B
4.6
NA
NA
NA
336X
10 Min.
ChIP- Seq (3 human samples)
Illumina
3,101
106 M
1,273
36
NA
1.5 Hrs.
RNA-Seq (6 human samples) Data provided by Illumina.
Illumina
3,101
322 M
2,687
50
NA
3.5 Hrs.
RNA-Seq (2 human samples) Data provided by Ion Torrent.
Ion Torrent
3,101
17.5 M
875
100
NA
1.5 Hrs.

SeqMan NGen de novo Assembly Benchmarks
Data Set
Sequence Technology
Number of Reads (K)
Number of Bases (M)
Coverage

Assembly Time**

K-12 E. coli Genome*
Illumina
2,500
250
51X
100
17 Min.
"Deep" K-12 E. coli Genome* Illumina 10,000 4,539 205X
82
1.5 Hrs.
K-12 E. coli Genome*
Roche 454
1,075
606
30X
26
18 Min.
K-12 E. coli Genome (merge pair data) Data provided by Ion Torrent.
Merged pair data consists of overlapping forward and reverse reads.
SeqMan NGen aligns these reads and merges them into a single consensus.
Ion Torrent
3,978
387
100X
12
2 Hrs.
K-12 E. coli Genome (mate pair data) Data provided by Ion Torrent.
Ion Torrent
7,077
1,826
150X
34
3.5 Hrs.
Rodent Transcriptome*
Roche 454
1,064
570
16X
1,199
5.5 Hrs.

 

*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.