How long does it take to assemble and call variants?

This depends whether you are doing the assembly on your local computer or are using DNASTAR Cloud Assembly. Depending on hardware and depth of sequences, local whole-genome resequencing can take as little as 5 minutes for a bacterial assembly to 24+ hours for a mammalian genome. A typical whole exome sequencing assembly takes between 30 and 90 minutes. Regardless of workflow, cloud assemblies are much faster and multiple assemblies can also be run simultaneously.

How do I compare variants between multiple samples?

Multiple sample variant analysis is done in ArrayStar, part of Lasergene Genomics. Variant samples can be compared and filtered into sets of interest using customizable tables, a filter wizard, Venn diagram, heat map or scatter plot.

What supplemental variant data is available in the Variant Annotation Database?

For human resequencing data, DNASTAR provides access to the Variant Annotation Database, which contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations include information about the frequency of the variant in the general population, in specific populations, and in publications, as well as information concerning the variant’s impact on functionality. The annotation information comes from several sources, including:

• Mastermind, the comprehensive database of genomic literature from Genomenon, providing access to NGS variant data from millions of PubMed publications.
• 1000 Genomes Project and the Exome Sequencing Project (ESP)
• dbNSFP v 4.1 which includes:

• Functional impact predictions from Sorting Intolerant from Tolerant (SIFT), MutationTaster, and the Likelihood Ratio Test (LRT).
• Evolutionary conservation scores from SiPhy, PhyloP, PhastCons and GERP++.
• Pathogenicity and clinical significance impact from ClinVar.
• Basic amino acid sequence information, Database of Single Nucleotide Polymorphism (dbSNP) IDs, and annotations from Uniprot and Interpro.

Can I import other annotation data into my variant analysis project?

Yes, you can import most any annotation data in text format, including gene and SNP level annotation data.

What types of variant analysis are available post-assembly?

Lasergene Genomics provides a wide variety of variant analysis tools, including:

• Large-scale SNP comparisons across individuals and groups
• Advanced gene filtering based on the level of disruption to each gene caused by variations
• Comparison of groups of variants using text filters, tabular data, or graphical representations that include Venn diagrams, scatter plots and heat maps
• The ability to send genes or variants of interest to SeqMan Ultra to view the read alignment at that position; or to GenVision Pro to view the assembly coverage for all samples simultaneously

Can Lasergene Genomics detect structural variations in genomic resequencing data?

Yes, Lasergene Genomics can detect copy number variation (CNV) and other structural variants as part of gene panel, whole exome and whole genome sequence analysis. Simply check the box for Calculate Copy Number Variation during assembly setup in SeqMan NGen. You can then view, filter and analyze CNVs and other structural variants using ArrayStar and SeqMan Pro.

Does Lasergene Genomics support BED or VCF files for targeted sequencing?

Yes. SeqMan NGen can read and utilize BED and VCF files in the assembly and can also create and export a VCF file during assembly. ArrayStar can export BED and VCF files.

Can I use VCF files created from another NGS software pipeline?

Yes, any VCF file in standard format is compatible. You will need to provide the same genome reference sequence (or genome version) along with the VCF files when you set up your variant analysis project in SeqMan NGen.

What advantages does DNASTAR provide for analyzing my VCF files?

We provide enriched variant analysis for VCF files including the ability to:

1. Easily analyze and compare large number of variants across multiple samples.
2. Comprehensively compare groups of variants using text filters, tabular data, or graphical representations that include Venn diagrams, scatter plots, and heat maps.
3. Import additional database annotation/information that may be lacking in your VCF file. For example, most VCF files lack information regarding a variant’s effect on protein coding, but by providing the reference genome, SeqMan NGen will calculate synonymous and non-synonomous variants. We provide access to our custom Genome Template Packages (available for many organisms) and Variant Annotation Database (available for human only), which add additional useful annotations like dbSNP IDs, GERP scores, genotype and allele frequencies, evolutionary conservation, clinical significance, and more.
4. Utilize a user-friendly interface for running the VCF file comparison and the analysis – no command line tools required.