De Novo Transcriptome Assembly


Lasergene Genomics Suite

DNASTAR's SeqMan NGen software has been rated #1 for de novo transcriptome assemblies in two 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


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

Next-Gen Software
For All Major Sequencing Technologies