SeqMan NGen

Category Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract Seqman NGen (SNG) was one of the first commercially available desktop software products specifically designed to assemble fragment data sequenced with Next Generation platforms from Illumina® and Roche 454® and/or conventional Sanger sequencing technologies.

Its integration with Lasergene (see G6G Abstract Number 20071) for analysis and visualization features provides users with a simple, advanced and economic tool to use with Next Generation sequencing data assembly and analysis.

Key Features of SNG include:

1) Desktop computer (Win or Mac) assembly for Illumina, Roche 454 and Sanger platform.

2) Assemble Genomic data up to 12 Mb in size.

3) Perform templated or de novo assemblies.

4) Perform hybrid (multi-platform) assemblies.

5) Assemble with coverage exceeding 10,000 X.

6) Discover single nucleotide polymorphisms (SNPs).

7) Integrated with popular Lasergene sequence analysis software to permit a wide range of sequence analyses and visualizations.

8) Full technical support by DNASTAR.

Annotating Template Sequence Prior to Assembly -- Prior to assembling your sequences in SNG, a user may annotate their template sequence in SeqBuilder, GeneQuest or SeqMan Pro for known SNPs/variations and other features.

SeqBuilder is the sequence editing and visualization application in the Lasergene suite. Assembling an annotated template sequence in SNG will enable the user to better analyze the identified putative SNPs when viewing the assembled project in SeqMan Pro.

User Defined Flexibility --

SNG offers complete flexibility in adjusting assembling parameters to meet the needs of your specific data set. Default parameter settings are also included to simplify analysis.

Since data sets and data types vary greatly, SNG offers the flexibility to adjust each assembling parameter to fit your data set.

In addition, users may select a number of preprocessing options, including vector and end-trimming along with the ability to exclude known repeats and contaminant sequences, such as primer reads, from your assembly.

1) SNP Detection and Reporting Management -

SNG permits users to manage both the number of passes to fill in SNP regions in a templated assembly and to set the minimum match percentage to use during the SNP fill in passes.

Depending on the project, such flexibility can be valuable in permitting focus on relevant SNPs.

2) Minimum Contig Size -

Users can establish the minimum number of sequences shown in a contig. After assembly, contigs (Not containing a template or reference sequence) with fewer sequences will be disassembled. The unassembled sequences can be saved into Fasta files.

3) View Assembly Results in Lasergene -

Following assembly in SNG, the saved project can be viewed in Lasergene's SeqMan Pro to analyze coverage and to identify SNPs. Your assembly will be displayed in the Project window.

If you choose to save the unassembled sequences in your assembly, they will be displayed in the Unassembled Sequences window.

4) View Areas Exceeding the Maximum Depth of Coverage -

SeqMan provides users with the option of entering a value for the Maximum Expected Coverage. Once this is done, it is easy to visualize areas that likely exceed this coverage parameter.

5) Strategy View -

By going to the Strategy View in SeqMan Pro, areas exceeding the desired Maximum Expected Coverage will be shown in Red.

6) Dual End Pair Characteristics -

SNG also permits users to set dual end pair specifier characteristics for the paired Sanger sequences in their assembly.

Pair specifiers define the naming convention for sequence pairs, as well as your requirement for a minimum and maximum distance between the opposite ends of your inserts. Forward and Reverse naming patterns for clones can also be included.

7) Exporting of Reports -

SNG 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.

System Requirements

Compatible with Windows® XP x64 and above and Mac OS X 10.4 and above.


Manufacturer Web Site SeqMan NGen

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G6G Abstract Number 20276

G6G Manufacturer Number 100770