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# WHOLE EXOME/WHOLE GENOME SEQUENCING ANALYSIS
Assemble whole genome, whole exome, and gene panel sequencing data against a reference sequence, then identify and compare variants.
## Let Lasergene Genomics do the heavy lifting of whole genome and whole exome sequencing analysis so you can focus on the results.
The sheer volume of data generated from whole exome sequencing and whole genome sequencing presents a challenge for many researchers faced with the prospect of assembling and analyzing it. Whether you are working with whole genome, whole exome, or other targeted sequencing data, the resulting amount of information requires a significant amount of data processing and analysis.  enables you to align resequencing data from all major NGS platforms against a reference sequence with unsurpassed ease and speed. Comprehensive post-assembly analysis options make it easy to  as well as structural and non-coding variants. Advanced gene filtering offers the ability to determine the level of disruption to each gene caused by variations. Handling large volumes of data is what Lasergene Genomics was designed to do – **let us do the heavy lifting**, so you can focus on the results.
## Whole exome/whole genome sequence analysis in 4 simple steps
## **Step 1**
Align data to a genomic template
## **Step 2**
Identify and compare variants of interest
## **Step 3**
Analyze variants within context of annotation data and read alignment
## **Step 4**
Evaluate assembly coverage for all sample simultaneously
## Learn more about **Whole Genome/Whole Exome Sequencing Analysis**
 |  |  |  |  | 
## Resources
Please see our resources below for more information on whole genome/whole exome sequencing analysis.
7 Steps for Human Variant Analysis
Identifying Candidate Variants and Their Effects on Protein Structure
A Next-Gen Sequencing Software Workflow for Gene Panel Validation Control
Automating Workflows in DNASTAR’s Lasergene Genomics Suite for High-Throughput Applications
DNASTAR’s SeqMan NGen vs. Four Alternative Pipelines: Variant Detection Comparison Using Illumina Data from NA12878
How Much Disk Space Do I Need For My Templated Genome Assembly?
Rapid, Large-Scale Prioritizing of Human Variants with Lasergene Genomics Suite
## Tutorials
Watch one of our videos or check out one of our  to learn more about whole genome sequence analysis and whole exome sequencing analysis.
#### Exome Analysis Tutorial
See how to align exome resequencing data from all major NGS platforms against a reference sequence with unsurpassed ease and speed in Lasergene Genomics. Comprehensive post-assembly analysis options make it easy to identify and compare genetic variants as well as structural and non-coding variants. Advanced gene filtering offers the ability to determine the level of disruption to each gene caused by variations.
#### Visualizing Genes and SNPS from ArrayStar in GenVision Pro
This quick tip video demonstrates how to visualize groups of genes or SNPs from ArrayStar in GenVision Pro.
#### Sanger Validation for NGS Assemblies
If you are working with next-gen sequencing, you may wish to use Sanger sequencing data to validate the results of the assembly or variant calls. Lasergene Genomics supports this validation, allowing you to combine both data types into a single project in SeqMan NGen.
#### Multiple Genome Assembly and Variant Analysis
In this video, learn how to align next-gen sequencing data for multiple samples to a genomic reference then perform variant analysis for all samples.
#### Using the Exome Coverage Report
This video guides you through using the Exome Coverage Report in SeqMan Pro.
#### Using the Variant Annotation Database
This video demonstrates how to use the Variant Annotation Database for human samples in Lasergene Genomics.
## FAQs
### 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 . Depending on hardware and depth of sequences, local whole genome…
This depends whether you are doing the assembly on your local computer or are using . 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.
Show more
### How do I compare variants between exomes?
Multiple sample whole exome sequencing analysis is done in .  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  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 , which contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations…
For human resequencing data, DNASTAR provides access to the , 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:
* , the comprehensive database of genomic literature from , providing access to NGS variant data from millions of PubMed publications.
*  and the 
*  v 4.1 which includes:
* Functional impact predictions from  (SIFT), , and the  (LRT).
* Evolutionary conservation scores from , ,  and .
* Pathogenicity and clinical significance impact from .
* Basic amino acid sequence information,  (dbSNP) IDs, and annotations from  and .
### 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…
* 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.
## Benchmarks
| Lasergene Genomics Reference-Guided Genome Alignment Benchmarks | | | |
| --- | --- | --- | --- |
| Data Set | Sequence Technology | Coverage | Assembly Time |
| Yeast Genome (ERX009559)\* | Illumina | 22X | 2 Minutes |
| Yeast Genome (srx1484451)\* | Ion Torrent | 22X | 3 Minutes |
| Drosophila Genome (SRX1961013)\* | Illumina | 23X | 23 Minutes |
| Human Exome (SRR701474)\* | Illumina | 81X | 53 Minutes |
| Mouse Rna-seq (SRX2013345)\* | Ion Torrent Proton | NA | 1.3 Hours |
| Human Rna-seq (SEQC-UHRR & Brain) | Illumina | NA | 1.6 Hours |
| Rice Genome (Srx179262)\* | Illumina | 34X | 1.6 Hours |
| Human Exome (SRX1873412)\* | Ion Torrent Proton | 162X | 3.9 Hours |
| Human Genome (SRP000239)\* | Illumina | 36X | 23 Hours |
## Citations
.  AJ,  T, Baldwin S, et al. (2024). Front. Cell. Infect. Microbiol., 15 April 2024. 
Chang, M.Y., Lee, C., Han, J.H. et al. (2018). BMC Med Genet 19, 29. 
Sousa, Alexandra et al. Portuguese Society of Cardiology, Volume 38, Issue 2, February 2019, Pages 129-139.
André Hallen, Arthur J.L. Cooper. bioRxiv 354100. 
Musharraf Jelani, Hannah C. Dooley, Andrea Gubas, et al. (2019). Brain, Volume 142, Issue 5, May 2019, Pages 1242–1254. 
Mutebi, John-Paul et al. (2018). Emerging infectious diseases, vol. 24,4 808–810. 17 Apr. 2018. 
Ready to learn more?
* A very powerful application
  *“It is a very powerful application; A run can be assembled with a reference genome in few minutes. SeqMan NGen is one of the best software applications of DNASTAR.”*
  Elisabeth Navarro, CNRS
* Easy and fast
  *“It is easy and fast to identify SNPs, structural changes, and CNVs.”*
  Kirk Nelson, Qpex Biopharma Inc.
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# Transcriptomics Workflows
Lasergene Genomics provides an automated pipeline for aligning and assembling RNA-Seq, ChIP-Seq, and de novo transcriptome data, getting you to comprehensive transcriptomic data analysis quicker.
 »  » Transcriptomics Workflows
## Let us do the work, so you can do yours.
Transcriptome analysis is crucial to connecting the information about a genome with its functional protein expression, but it’s often a cumbersome process with vast amounts of data requiring tedious project setup and time-consuming, complicated data manipulation.
 transcriptome analysis software removes these challenges through an automated pipeline that does the setup, assembly, and annotation work for you, so that you can get straight to comprehensive transcriptome analysis, including discovering novel transcripts, identifying differentially expressed genes, and evaluating gene ontology.
Our automated pipeline includes patented algorithms to handle virtually any size data set, access to diverse genome template packages, and integration with proprietary databases, to thoroughly and accurately prepare your transcriptome data. Use Lasergene Genomics to simplify transcriptome data analysis. Let us do the work, so you can do yours.
## Transcriptomics Workflows
* The best!
  *“Gene expression analysis in Arraystar is the best!”*
  Brenda Oppert, USDA ARS CGAHR
## Popular Resources
###### Article
###### Blog
## Transcriptomics Workflows FAQs
### Which Lasergene package do I need for transcriptome analysis?
 includes all the applications you need for our  and transcriptomics workflows. We also offer , our complete software package which includes…
 includes all the applications you need for our  and transcriptomics workflows. We also offer , our complete software package which includes , , and Lasergene Genomics. We offer both  and  for convenient annual licenses, which include upgrades and unlimited access to our technical support team.
### How do I access the transcriptome analysis workflows in Lasergene?
Our transcriptome analysis workflows can be accessed by clicking on the *Transcriptomics* tab in DNASTAR Navigator.
### What types of read technology are supported for transcriptome analysis?
Lasergene Genomics supports Illumina, Oxford Nanopore, PacBio, 454, Sanger/ABI and Ion Torrent sequencing technologies. For a full list of supported file types, see our  resource.
### Can I try before I buy?
Yes! We offer  of our complete  package. We also understand that transcriptome data analysis can be complex and sometimes overwhelming. We get…
Yes! We offer  of our complete  package. We also understand that transcriptome data analysis can be complex and sometimes overwhelming. We get it! That’s why we offer free, , customized to your specific research objectives, and led by our scientists on staff.