Lasergene Genomics Suite


Benchmarking Data


Listed below is representative Lasergene Genomics Suite 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.



 
Lasergene Genomics Suite Reference-Guided Genome Alignment 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 3,523 112,738 32 36X 23 Hrs.
8 Human Exomes* (multiplex) Illumina Hg19+dbSNP 27 1,268 12,047 76 446X 14 Hrs.
RNA-Seq (6 human samples) Illumina Hg19+dbSNP 3,101 322 2,687 50 NA 3.5 Hrs.
Human Exome* Illumina Hg19+dbSNP 27 163 12,390 76 459X 2 Hrs.
ChIP- Seq (3 human samples) Illumina Hg19+dbSNP 3,101 106 1,273 36 NA 1.5 Hrs.
RNA-Seq (2 human samples) Ion Torrent Hg19+dbSNP 3,101 17.5 875 100 NA 1.5 Hrs.
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.
"Deep" K-12 E. coli Genome* Illumina MG1655 5 45 4,539 100 908X 28 Min.
Ion AmpliSeqâ„¢ Cancer Panel (3 multiplexed data sets)Data provided by Ion Torrent. Ion Torrent Hg19+dbSNP 3,101 3 99 85 500X 24 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

3 387 115 77X 7 Min.
K-12 E. coli Genome* Roche 454 MG1655 5 1.5 606 400 121X 3 Min.
Fluidigm® Access Array System (2 multiplexed data sets)Data provided by Pacific Biosciences. Pac Bio Fluidigm human amplicons 0.1 < 1 7 180 500X 1 Min.
K-12 E. coli Genome* Illumina MG1655 5 2.5 250 100 50X 1 Min.


 
Lasergene Genomics Suite De Novo Assembly Benchmarks
Data Set Sequence Technology Number of Reads (K) Number of Bases (M) Coverage ContigN50 (Kbp) 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.