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 exomes?

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

How many exomes can I compare simultaneously?

At least 100 human exome data sets can be uploaded to a single ArrayStar project for comparison.

What types of files can I import for whole genome/whole exome sequencing analysis?

ArrayStar supports the import of SeqMan NGen assemblies (.assembly), files from other ArrayStar projects (.astar, .dmaproj), SeqMan Pro SNP files (.txt), VCF SNP files (.vcf), other text (.txt) and comma-separated value (.csv) files.

What supplemental data is available for variant analysis in whole exome/whole genome sequencing projects?

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.

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. SeqMan Pro can export VCF files.

Can I import other annotation data into my whole genome sequence 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?

• 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
• Send genes or variants of interest to SeqMan Pro to view the read alignment at that position; or GenVision Pro to view the assembly coverage for all samples simultaneously

What is the difference between whole genome sequencing and whole exome sequencing?

Whole exome sequencing analysis includes only the protein-coding region of genes in the assembly. Whole genome sequence analysis includes the entire genome in the assembly. Lasergene Genomics applications can handle both types of assembly and analysis.

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.

Can I analyze VCF data for my whole exome/whole genome sequence analysis project?

Yes, you can analyze both raw sequencing data as well as VCF variant data for genome resequencing projects in Lasergene. When starting from VCF data, Lasergene will classify called variants by their effect on coding regions, relative to the imported reference genome.