SeqMan NGen- Next-Gen Sequence Assembly Software, De Novo Sequence Assembly Software, Reference-Guided Alignment Software
SeqMan NGen Rated #1 for Assembling Illumina and 454 Data

SeqMan NGen - Software for Next-Gen Sequence Assembly

SeqMan NGen is groundbreaking sequence assembly software that has the ability to assemble any size genome quickly and accurately on a desktop computer. How quickly? Check out our benchmarking data. How accurately? Check out our enhanced SNP prediction accuracy. SeqMan NGen assembles data from all major next-gen sequencing platforms, and provides an extremely easy-to-use interface that steps you through your sequence assembly and analysis project. SeqMan NGen is fully integrated with Lasergene's SeqMan Pro, so that once your assembly is complete, you can continue with downstream analysis including discovering SNPs using Bayesian statistical models, identifying large insertions and deletions, evaluating coverage, and annotating your consensus sequence. SeqMan NGen also assembles RNA-Seq, ChIP-Seq, and miRNA data, allowing easy, integrated, post-assembly analysis in ArrayStar with QSeq of both gene expression and SNP data. To learn more, see the Features or Resources tab below.


"SeqMan NGen is a very powerful application; a 454 run can be assembled to a reference genome in just a few minutes."

Elisabeth Navarro, CNRS


Supported Workflows

  • Reference-guided assemblies for any size genome
  • De novo genome and transcriptome assemblies
  • Cancer genomics and clinical research
  • Gene panel assembly, validation, and analysis
  • Targeted re-sequencing/exome assemblies to identify low frequency SNPs and variants
  • Metagenome and population assemblies and variant analysis
  • 16S rRNA alignment and analysis
  • Host-virus integration analysis with automatic filtering of host data from mixed samples
  • Large-scale, multi-sample SNP analysis
  • RNA-Seq assemblies with integrated gene expression and SNP analysis
  • ChIP-Seq and miRNA assemblies

    Fast and Accurate Assembler

  • SeqMan NGen is >99.8% accurate for SNP prediction. Learn more.
  • Perform bacterial genome assemblies with automated gap closure.
  • Take advantage of optimized assembly parameters for each of your projects, as well as the freedom to make adjustments if desired.Video See it!
  • Use paired-end sequence information during assembly, as well as for downstream analysis and contig ordering.
  • Assemble multiple samples against a single reference simultaneously for post-assembly SNP comparison between individuals and groups of individuals.

    Post-Assembly Analysis

  • Perform SNP and genotype calling in haploid and diploid organisms using Bayesian statistical models Video See it!
  • Compare SNP and small indels to dbNSFP, dbSNP, COSMIC, and GERP databases during assembly for all major model organisms Video See it!
  • Utilize the structural variant report for identifying large insertions and deletions as well as small indels in reference-guided assemblies
  • Analyze coverage depth, group contigs into scaffolds, and annotate your consensus Video See it!

    Input/output Files

  • Import data from all major next-gen and third-gen platforms, including Illumina, Roche 454, Pacific Biosciences, SOLiD, and Ion Torrent.
  • Input multiplexed samples using standardized tag sets or user-defined custom tags.
  • Save your project as a BAM or ACE file.
  • Export your project to GenVision for a publication-quality graphical image of the assembly.
  • Resources

    Try It

    Try SeqMan NGen for Free!

    Request a fully functional free trial of Lasergene Genomics Suite to try it out for yourself.


    Free Trial for Windows

    Free Trial for Macintosh

    Free Trial for Linux - Ubuntu

    Buy It

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    To purchase Lasergene Genomics Suite, please fill out our brief quote request form. A member of our dedicated sales team will respond to you within one business day.