Product News: DNASTAR’s New SeqMan NGen provides Powerful Assembly Tool for Next Generation Sequencing Platforms

14 Oct 2008

The latest version of next Generation Sequencing Assembly tools from DNASTAR, SeqMan NGen v1.2, offers users additional capacity and features for use with the Roche 454®, Illumina® and Helicos® sequencing platforms. The software is designed for use with either Windows (XP or Vista) or Macintosh (OS 10.4 or 10.5) operating systems. A main feature of the software is its ability to interface with the popular Lasergene sequence analysis software for analysis functions. This provides users with the advantage that they can use one software package for all of their sequencing analysis needs.

SeqMan NGen offers complete flexibility in adjusting assembling parameters to meet the needs of your specific data set. Users may also decide on a number of preprocessing options, including vector and end-trimming, marking known repeats, and excluding contaminant sequences, such as primer reads, from their assembly.

Data sets can be assembled de novo, or with a template sequence. Multiple templates can also be used if desired. Annotating template sequences in SeqBuilder for known SNPs, CDSs, and other features prior to assembly will enhance the analysis of identified putative SNPs in SeqMan Pro. Following a templated assembly, any remaining unassembled sequences can be assembled into contigs, if desired. DNASTAR recommends using dual end data, if available, when assembling a data set de novo.

SeqMan NGen offers three output options for saving your finished assembly: the SeqMan Pro project file format, as a Phrap assembly, and in FASTA format. Following assembly in SeqMan NGen, saved projects can be viewed in Lasergene for analysis, including identifying SNPs and analyzing coverage.

SeqMan NGen can also export a report summarizing your assembly statistics, including the number of assembled/unassembled (matched/unmatched) sequences and contigs in your project, the parameters used, the average quality scores, and the number of sequences excluded from the assembly due to exceeding the maximum coverage parameter.

Free Trial versions of SeqMan NGen are available to interested users by going to the DNASTAR website and selecting “Request a Free Trial”.