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METAGENOMIC ASSEMBLY

Assemble metagenomic sequencing data de novo or against thousands of bacterial genomic templates, then perform comprehensive microbiome analysis. PRICING DOWNLOAD FREE TRIAL

Use Lasergene Genomics’ powerful algorithms to align metagenomic sequence data to a diverse reference data set or cluster novel sequences for identification.

Effectively assembling and analyzing metagenomic sequencing data can be challenging, considering the volume of data involved, as well as the many time-consuming steps often required to identify variants, calculate coverage, and remove host DNA. Lasergene Genomics simplifies the process by providing a wizard to walk you through the metagenomic assembly and host removal process from start to finish. Our microbiome analysis software makes it easy to align metagenomic sequencing data to thousands of whole annotated bacterial genomes from NCBI, or to a 16s rRNA database. The powerful algorithms within SeqMan NGen perform metagenomic assemblies with unprecedented speed, getting you from raw data to the analysis stage quicker. SeqMan NGen also offers the ability to perform a metagenomic assembly of novel sequences de novo, or assemble de novo highly variable sequences from HLA, antibody regions, viral populations, or mitochondrial populations. Variant detection and coverage calculations are done automatically for you during the metagenomic assembly process, so that following the assembly, you are ready to analyze contigs, and easily identify which bacterial strains are most abundant in the microbiome.

Heat Map
A heat map in ArrayStar, visualizing the relative abundance of bacterial strains between healthy and symptomatic samples.

Metagenomics assembly in 4 simple steps

Metagenomic Assembly Step 1

Step 1

Set up and run the metagenomic assembly

Metagenomic Assembly Step 2

Step 2

Identify strains most abundant in the sample

Metagenomic Assembly Step 3

Step 3

Analyze variants and evaluate coverage

Metagenomic Assembly Step 4

Step 4

Visualize relative abundance of bacterial strains

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Learn more about Metagenomic Assembly

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on metagenomic sequence analysis.

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Metagenomic Sequencing and Analysis

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Cloud Assemblies for NGS Sequences Webinar

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Considerations for Next-Gen Sequence Assembly and Analysis Software Selection

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How Much Disk Space Do I Need For My Templated Genome Assembly?

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Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about using our microbiome analysis software.

Metagenomic Assembly with Host Removal

This video demonstrates how to perform a metagenomic assembly in Lasergene Genomics, including how to remove host DNA.

Assembly and Alignment of 16S Data

This video demonstrates how to identify the presence of various species in a complex sample, based on short regions on rRNA.

Lasergene Genomics Overview

This video gives an overview of Lasergene Genomics, which provides everything you need for assembly, alignment, and analysis of transcriptome and genome sequencing data, all in a single integrated package.

Variant Analysis Overview

This video demonstrates the Lasergene Genomics automated pipeline, which assembles your reads to a template, performs variant calling, and then compares the variants across multiple samples, all without human intervention.

FAQs

Where do I find bacterial genome reference genomes for my metagenomic assembly?

When setting up your metagenomic assembly project, we provide several options for defining your bacterial reference genomes. You can:…

When setting up your metagenomic assembly project, we provide several options for defining your bacterial reference genomes. You can:

  • Use the Microbial Genome Database genome template package we provide that contains all of the NCBI reference bacterial genomes.
  • Use the NCBI genome downloader that is integrated with SeqMan NGen to download multiple bacterial genomes.
  • Add your own bacterial genome reference sequences.
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Can I align my metagenomic sequence data to a 16S ribosomal RNA database?

Yes, you can align your metagenomic sequence data to 16S ribosomal RNA databases, although we do not provide a genome template for these databases. To perform a metagenomic assembly with a 16S…

Yes, you can align your metagenomic sequence data to 16S ribosomal RNA databases, although we do not provide a genome template for these databases. To perform a metagenomic assembly with a 16S rRNA database, first download the 16S database from its source in FASTA format, and then specify it as your set of reference sequences in the Input Biome Genomes screen of the SeqMan NGen wizard.

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How do I compare multiple metagenomic samples?

SeqMan NGen allows you to easily set up multiple metagenomic assemblies.  Simply choose Multi-sample as your Experiment setup in the Input Sequences screen of the SeqMan NGen wizard, then…

SeqMan NGen allows you to easily set up multiple metagenomic assemblies.  Simply choose Multi-sample as your Experiment setup in the Input Sequences screen of the SeqMan NGen wizard, then group your metagenomic sequencing data into experiments. SeqMan NGen will automatically calculate variants and genome coverage for downstream analysis.

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What applications do I use for analyzing my completed metagenomic assembly?

After completing a metagenomic assembly in SeqMan NGen, use SeqMan Ultra to analyze variants, evaluate coverage, and quickly identify which bacterial strains are most abundant in the sample….

After completing a metagenomic assembly in SeqMan NGen, use SeqMan Ultra to analyze variants, evaluate coverage, and quickly identify which bacterial strains are most abundant in the sample. Use ArrayStar to generate a heat map, to visualize the relative abundance of bacterial strains across multiple samples.

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Citations

Detection of a Novel Astrovirus in Brain Tissue of Mink Suffering from Shaking Mink Syndrome by Use of Viral Metagenomics.
Blomström, Anne-Lie, Widén, Frederik, Hammer, Anne-Sofie, Belák, Sándor, Berg, Mikael. Journal of Clinical Microbiology Nov 2010, 48 (12) 4392-4396; DOI: 10.1128/JCM.01040-10.

Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression.
McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, Rohwer F, Paul JH. PLoS One. 2008;3(9):e3263. Published 2008 Sep 23. doi:10.1371/journal.pone.0003263.

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes.
Ng TF, Willner DL, Lim YW, et al. PLoS One. 2011;6(6):e20579. doi:10.1371/journal.pone.0020579.

Metagenomic analysis of viruses in reclaimed water.
Rosario, K., Nilsson, C., Lim, Y.W., Ruan, Y. and Breitbart, M. Environmental Microbiology. 2009;11: 2806-2820. doi:10.1111/j.1462-2920.2009.01964.x.

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    Dr. Andrew M. Kropinski, University of Guelph

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