DNASTAR Next-Gen Sequencing Software Solutions
SeqMan NGen Best for de novo Transcriptome Assemblies

De Novo Transcriptome Assembly

DNASTAR's SeqMan NGen software has been rated #1 for de novo transcriptome assemblies in two recent peer-reviewed articles published by BMC Genomics. Both studies compared SeqMan NGen with other products in performing a de novo transcriptome assembly – one study used 454 data; the other study used Illumina data.  Both studies came to the same conclusion – DNASTAR SeqMan NGen is the best software for performing de novo transcriptome assemblies. Learn More.


SeqMan NGen is part of the Lasergene Genomics Suite. Features of this software enable you to:

  • Trim EST and transcriptome sequence data of all contaminating linkers, primers and vectors
  • Align Ion Torrent, Roche 454, Illumina, Pacific BioSciences, and Sanger single and paired-end data using a palette of adjustable parameters
  • Visualize a coverage histogram of assembled sequences and perform SNP and variant analysis
  • Identify new mRNA via batch BLAST and export of consensus sequences
  • For more information on using Lasergene Genomics Suite for your de novo transcriptome 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 Transcriptome Assembly Benchmarks
    Data Set
    Sequence Technology
    Number of Reads (K)
    Number of Bases (M)

    Assembly Time**

    Rodent Transcriptome*
    Roche 454
    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.