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VIRAL GENOME ANALYSIS

Quickly and easily align reads and identify variants, with comprehensive support for PCR-amplified long read fragments from ARTIC Network protocols. PRICING DOWNLOAD FREE TRIAL

Quickly identify new viral strains.

Going from raw viral genome sequencing data to the eventual identification of new viral strains can be labor-intensive process. With fast-evolving viruses, being able to analyze data quickly is essential. Our viral genome sequencing analysis workflow is available for both Sanger and NGS data, and also includes comprehensive support for PCR-amplified fragments generated using the ARTIC Network protocols. We’ve streamlined this sometimes complicated process so that you can get to the analysis phase quicker. Start by assembling your viral genome sequencing data in SeqMan Ultra to evaluate variants and generate consensus sequences for each sample, then quickly align large groups of genomes in MegAlign Pro with known strains to easily identify and compare variants in the alignment.

Distance+table+of+viral+genome+alignment+in+MegAlign+Pro

Viral genome sequencing analysis in 4 simple steps

Viral Genome Sequencing Analysis Step 1

Step 1

Assemble single or multiple viral samples against a reference sequence in SeqMan Ultra

Viral Genome Sequencing Analysis Step 2

Step 2

Evaluate variants and export consensus sequences for samples of interest

Viral Genome Sequencing Analysis Step 3

Step 3

Align large groups of consensus sequences to known strains in MegAlign Pro

Viral Genome Sequencing Analysis Step 4

Step 4

Analyze statistics and identify variants in the alignment

computer

Learn more about Viral Genome Sequencing Analysis

Resources | Tutorials | FAQs | Citations

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Resources

Please see our resources below for more information on viral genome sequencing analysis.

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Using the MAFFT alignment algorithm for high-capacity viral genome alignment

Read Blog Post

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Webinar: Master Viral Genome Analysis

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SeqMan Ultra Help

User Guide

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SeqMan NGen Help

User Guide

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MegAlign Pro Help

User Guide

Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about viral genome sequencing analysis.

Viral Genome Assembly & Analysis (including ARTIC protocol samples)

If you have raw viral genome data from Nanopore or PacBio, this video shows step-by-step how to assemble your reads to a template and then analyze the results in ArrayStar, SeqMan Ultra and/or MegAlign Pro. Alternatively, if you have draft genomes from the ARTIC or a similar protocol, you can jump right in at the MegAlign Pro step. This video shows both starting points.

FAQs

What sequence technologies do you support for viral genome sequencing analysis?

For viral genome analysis, we support Illumina, Ion Torrent, and Sanger/ABI sequencing technologies, as well as long reads from Oxford Nanopore and PacBio, including data generated using the ARTIC Network protocols.

Where can I get my reference sequence?

A reference sequence for assembling your viral genome sequencing reads can be downloaded directly from NCBI during project set up…

A reference sequence for assembling your viral genome sequencing reads can be downloaded directly from NCBI during project set up.

From the Reference Sequence step, click on Download NCBI Genomes, then either browse available genomes, or enter the accession number for the genome you wish to download.

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How do I access the viral genome sequencing analysis workflow?

To access the viral genome sequencing analysis workflow, first launch SeqMan Ultra and choose New Assembly.  Then, choose from one of the following:

To access the viral genome sequencing analysis workflow, first launch SeqMan Ultra and choose New Assembly.  Then, choose from one of the following:

  1. If you have long read data from Oxford Nanopore or PacBio, choose ARTIC amplicon under the Genomics section.
  2. If you have short read NGS data from Illumina or Ion Torrent, choose Variant analysis and resequencing under the Genomics section, then choose NGS-Based > Whole Genome from the resulting SeqMan NGen wizard.
  3. If you have Sanger/ABI data, choose Variant analysis and resequencing under the Genomics section, then choose ABI/Sanger > Whole Genome from the resulting SeqMan NGen wizard.

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How do I align my assembled genomes to known strains?

You can align the consensus sequences for your assembled reads to known viral strains using MegAlign Pro. To do this, first export your consensus sequences from…

You can align the consensus sequences for your assembled reads to known viral strains using MegAlign Pro. To do this, first export your consensus sequences from SeqMan Ultra by selecting File > Export Data > Consensus. Then, add these exported consensus sequences to MegAlign Pro along with known strains (publicly available from NCBI). After adding all of the sequences you wish to align, select Align > Align Using MAFFT.

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Which Lasergene package do I need to perform the viral genome analysis workflow?

If you are starting with raw, unassembled reads, you will need Lasergene Genomics to assemble your sequencing data and generate consensus sequences…

If you are starting with raw, unassembled reads, you will need Lasergene Genomics to assemble your sequencing data and generate consensus sequences. You will need Lasergene Molecular Biology to access MegAlign Pro for aligning your assembled genomes to known strains and identifying variants. Both Lasergene Genomics and Lasergene Molecular Biology are included in the full DNASTAR Lasergene package. If you already have draft genomes that you wish to align to known strains, then you will only need the Lasergene Molecular Biology package.

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Citations

Full length genomic sanger sequencing and phylogenetic analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Nigeria.
Shaibu JO, Onwuamah CK, James AB, Okwuraiwe AP, Amoo OS, Salu OB, et al. PLoS ONE 16(1): e0243271. https://doi.org/10.1371/journal.pone.0243271

Whole-Genome Sequences of SARS-CoV-2 Lineage B.1.525 Strains (Variant η) Detected from Patients in the Abruzzo Region (Central Italy) during Spring 2021.
Delli Compagni E, Mangone I, Bonfini B, Di Gennaro A, Teodori L, Leone A, Casaccia C, Portanti O, Averaimo D, Zilli K, Malatesta D, Ancora M, Scialabba S, Di Domenico M, Lorusso A. 2021. Microbiol Resour Announc 10:e00618-21. https://doi.org/10.1128/MRA.00618-21

In-House, Rapid, and Low-Cost SARS-CoV-2 Spike Gene Sequencing Protocol to Identify Variants of Concern Using Sanger Sequencing.
Fatimah S. Alhamlan, Dana M. Bakheet, Marie F. Bohol, Madain S. Alsanea, Basma M. Alahideb, Faten M. Alhadeq, Feda A. Alsuwairi, Maha Al-Abdulkareem, Mohamed S. Asiri, Reem S. Almaghrabi, Sarah A. Altamimi, Maysoon S. Mutabagani, Sahar I. Althawadi, Ahmed A. Alqahtani. medRxiv 2021.08.09.21261723; doi: https://doi.org/10.1101/2021.08.09.21261723

Molecular analysis of the 2012 Bundibugyo virus disease outbreak.
Hulseberg, Christine E. et al. Cell Reports Medicine, Volume 2, Issue 8, 100351

A new coronavirus associated with human respiratory disease in China.
Wu, F., Zhao, S., Yu, B. et al. Nature 579, 265–269 (2020). https://doi.org/10.1038/s41586-020-2008-3

A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Zhou, P., Yang, XL., Wang, XG. et al. Nature 579, 270–273 (2020). https://doi.org/10.1038/s41586-020-2012-7

Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments.
Yashpal Singh Malik, Shubhankar Sircar, Sudipta Bhat, Khan Sharun, Kuldeep Dhama, Maryam Dadar, Ruchi Tiwari & Wanpen Chaicumpa (2020). Veterinary Quarterly, 40:1, 68-76, DOI: 10.1080/01652176.2020.1727993

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Problem solved

“The software works very well and is very easy to handle. I believe many people have a problem with handling Oxford Nanopore data, because the sequencing itself is easy to handle in every lab, which is a big advantage (time and money), but many small labs like us have no bioinformatics for data analysis. With DNASTAR this problem can be solved.”

Dr. Olav Grundmann, Impetus GmbH & Co. Bioscience KG

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