Genome Alignment Software

Reference-Guided Genome Alignment Software

Lasergene Genomics Suite

DNASTAR's Lasergene Genomics Suite includes genome alignment software which enables you to align data from all major next-gen sequencing platforms against a reference sequence with unsurpassed ease and speed. Features of the Lasergene Genomics Suite software include:

  • Quick and accurate alignment of human or other large eukaryotic genomes against a genomic template on a desktop computer - check out our benchmarks below.
  • The ability to assemble genomic data from virtually any next-gen sequencing platform, including  Illumina, Ion Torrent, Pacific Biosciences, or Sanger data.
  • An interactive, data-rich SNP report, including probabilities and genotypes determined with Bayesian statistics as well as dbSNP/COSMIC/GERP associations
  • The option to generate output of the finished assembly in BAM format

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Lasergene Genomics Suite Reference-Guided Genome Alignment Benchmarks
Data Set Sequence
Size (Mbp)
Number of
Reads (M)
Number of
Bases (Mbp)
Length (bp)
Coverage Assembly
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.
"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


3 387 115 77X 7 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.

*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.

Next-Gen Software For All Major Sequencing Technologies