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De Novo Genome Assembly

DNASTAR's Lasergene Genomics Suite includes de novo sequence assembly software that allows users to quickly and easily perform de novo assemblies using either long or short reads from all major next-gen sequencing platforms. Features of the Lasergene Genomics Suite software include:

  • Quick and accurate de novo assembly on a desktop computer
  • Assembly of either single-end or paired-end data
  • The ability to view contig scaffolds along with the paired sequences that tie the contigs together
  • Annotation of gaps in the scaffold consensus
    • For more information on using Lasergene Genomics Suite for your de novo assembly projects, this brief video gives an overview of the workflow:

     

    Request a fully-functional, free trial of Lasergene Genomics Suite.

     

     

    Lasergene Genomics Suite De Novo Genome 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.