SeqMan Pro - Software for Contig Assembly and Analysis, Including SNP Discovery, Coverage Evaluation, and Project Annotation
Lasergene’s SeqMan Pro offers quick and accurate sequence assembly and analysis of Sanger data, in addition to providing visualizations and analysis of next-gen projects assembled by SeqMan NGen. Discover SNPs, analyze coverage, annotate your consensus, and much, much more. To learn more, see the Features or Resources tabs below.
"SeqMan Pro has proven to be invaluable to our lab for assembling and editing sequencing projects using capillary sequence data from the ABI 3130 and 3730 sequencing platform. This is one of those applications that just works like it should."
Kevin Kunstman, Northwestern University Medical School
Features
Assemble Contigs
Assemble your de novo or reference-guided Sanger sequence data. You can also view your next-gen or third-gen sequence assembly from a SeqMan NGen assembly in SeqMan Pro.
Paired-end data support for Sanger, Illumina, Ion Torrent, and Roche 454 data from a SeqMan NGen assembly to visualize the orientation and distance between contigs.
Assemble certain groups of sequences separately, each into its own contig using the Assemble in Groups feature.
Discover SNPs
Live, interactive SNP reports allow you to view information about a putative SNP while at the same time, viewing it in the context of the Alignment View.  See it!
Multiple filters enable you to control which SNPs to review. For example, you may show only SNPs that occur a certain distance from a coding feature, show only novel SNPs, or show only SNPs that occur within a certain depth of coverage. See it!
Save selected SNPs from your project in a custom SNP table for use in subsequent assemblies.
Mutliplex support for assemblies created in SeqMan NGen allows you to view SNPs on a per sample basis.
Annotate your Project
Easily copy features from constituent sequences to the consensus sequence. See it!
Add features to the consensus sequence through BLAST searching. See it!
Annotate sequence files with features prior to assembly to display them in the Alignment View.
Save or export the consensus sequence to SeqBuilder to see SeqMan Pro's auto-annotation of features for areas of high and low coverage, as well as confirmed SNPs. See it!
Analyze Coverage and Identify Structural Variants
Use the Coverage Threshold and Depth of Coverage graphs to view coverage within the assembly and compare it to the threshold parameters. See it!
View coverage and RPKM values for targeted regions in exome capture projects.
Choose locations to drive the closure or to fill in areas of low coverage using the Primer Walking feature. See it!
Utilize the structural variant report for identifying large insertions and deletions, as well as small indels, in reference-guided assemblies
Export Data for Further Analysis
Export the consensus sequence for one or more contigs, with or without gaps and layout features (representing each constituent sequence). If desired, you may limit the export to a range of the consensus.
Export the consensus sequence to SeqBuilder for designing primers for regions of low coverage, automatically annotated by SeqMan Pro.
Export SNP data to ArrayStar for large-scale SNP comparisons and gene-impact analysis between multiple individuals and groups
Export your project to GenVision for a publication-quality graphical image of the assembly.
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