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	Hg19+dbSNP	27	163	12,390	76	459X	2 Hrs.
Ion AmpliSeq™ Cancer Panel (3 multiplexed data sets) Data provided by Ion Torrent.	Ion Torrent	Hg19+dbSNP	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	Hg19+dbSNP	3,101	106 M	1,273	36	NA	1.5 Hrs.
RNA-Seq (6 human samples) Data provided by Illumina.	Illumina	Hg19+dbSNP	3,101	322 M	2,687	50	NA	3.5 Hrs.
RNA-Seq (2 human samples) Data provided by Ion Torrent.	Ion Torrent	Hg19+dbSNP	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	ContigN50 (Kbp)Minimum contig size where at least 50% of all the sequence data is represented	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.

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