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DE NOVO TRANSCRIPTOME ASSEMBLY

Perform de novo transcriptome assembly with auto-annotation using DNASTAR’s patented algorithm which utilizes RefSeq to identify and merge transcripts, resulting in longer, more complete mRNA sequences. PRICING DOWNLOAD FREE TRIAL

Simplify de novo transcriptome assembly using the automated pipeline in Lasergene Genomics.

De novo transcriptome assembly is a powerful technique in the study of non-model organisms, but transcriptomics data analysis often presents significant challenges due to the vast amounts of data and the common difficulties faced when removing contaminants, identifying and annotating transcripts, and using assembled transcripts in downstream analysis. Lasergene Genomics’ transcriptome assembly tools present solutions to all of these issues. Our patented clustering and assembling algorithms can handle virtually any size data set on a desktop computer, eliminating the need for super-computing clusters. Lasergene Genomics automatically removes the most common adapters, as well as any user-specified contaminant sequences, and provides access to our proprietary Transcript Annotation Databases, which use transcript annotations from RefSeq, facilitating assembly and annotation of even the most novel organisms. Once the de novo transcriptome assembly is complete, we provide FASTA files of both identified transcripts and novel transcripts, fully annotated and ready to use in downstream analysis, including using as a reference set for RNA-Seq analysis.

Heat Map
An Arraystar heat map visualizing differential gene expression in two Brassica tissue types. The RNA-Seq Brassica data was assembled against identified transcripts from a de novo transcriptome assembly run in SeqMan NGen.

De novo transcriptome assembly in 4 simple steps

De Novo Transcriptome Assembly Step 1

Step 1

Specify contaminant sequences

De Novo Transcriptome Assembly Step 2

Step 2

Add your de novo transcriptome reads

De Novo Transcriptome Assembly Step 3

Step 3

Choose a Transcript Annotation Database and run assembly

De Novo Transcriptome Assembly Step 4

Step 4

Use novel or identified transcripts as a reference set for RNA-Seq assembly and gene expression analysis

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Learn more about De Novo Transcriptome Assembly

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on de novo transcriptome assembly.

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Tips for Successful Transcriptome Sequence Assembly

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Lasergene Genomics Overview

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Is Open Source NGS Software for You?

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Considerations for Next-Gen Sequence Assembly and Analysis Software Selection

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Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about de novo transcriptome assembly.

De Novo Transcriptome Assembly and Auto-Annotation in Lasergene

See how to assemble de novo transcriptome data in Lasergene, and utilize our auto-annotation capability to get more complete transcripts than ever before. Then, use the results as a reference set for RNA-Seq analysis.

RNA-Seq Alignment and Analysis in Lasergene Genomics

This video demonstrates how Lasergene Genomics makes it easy to align and analyze your RNA-Seq data.

Creating Gene Sets and Comparing in the Venn Diagram

See various ways to filter and create gene sets of interest, then compare the gene sets in the Venn diagram in ArrayStar.

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.

Tips for Successful De Novo Transcriptome Sequence Assembly Using RNA-Seq Data

De novo transcriptome assembly presents some unique challenges.
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FAQs

What applications do I need to perform a de novo transcriptome assembly?

All of the applications you need for a de novo transcriptome assembly are included in Lasergene Genomics. SeqMan NGen is the assembler, and also provides the wizard for setting up your de novo transcriptome assembly project. ArrayStar is the application used for downstream gene expression analysis.

What types of read technology are supported for a de novo transcriptome assembly?

SeqMan NGen supports all major NGS technologies, including Illumina, Ion Torrent, Roche 454, and Pacific Biosciences,

How do I annotate my transcripts?

Lasergene Genomics automatically annotates your assembled transcripts using transcript annotations extracted from NCBI’s RefSeq database and allows comparison to either the complete database, or a subset of data that you specify within SeqMan NGen when you set up your de novo transcriptome assembly project.

What output files are generated from my de novo transcriptome assembly?

Following your de novo transcriptome assembly, two FASTA files will be created and saved to your specified output directory. One FASTA file contains identified annotated transcripts, and the other contains novel transcripts.

How do I use my transcripts for an RNA-Seq alignment project?

You can use your identified transcripts or novel transcripts as templates for aligning RNA-Seq data simply by adding the desired FASTA file(s) in the Reference Sequence section of the SeqMan NGen wizard when creating your RNA-Seq project.

Citations

Comparative De Novo Transcriptome Assembly of Notophthalmus viridescens RNA-seq Data using Two Commercial Software Programs
Chacon J, Cuajungco MP. Calif J Health Promot. 2018;16(1):46–53. doi:10.32398/cjhp_20181601.

Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species
Lorenz, W.W., Ayyampalayam, S., Bordeaux, J.M. et al. Tree Genetics & Genomes 8, 1477–1485 (2012). https://doi.org/10.1007/s11295-012-0547-y.

De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence
Comeault, A.A., Sommers, M., Schwander, T., Buerkle, C.A., Farkas, T.E., Nosil, P. And Parchman, T.L. (2012),  Molecular Ecology Resources, 12: 549-561. doi:10.1111/j.1755-0998.2012.03121.x.

An integrated transcriptome-wide analysis of cave and surface dwelling Astyanax mexicanus
Gross JB, Furterer A, Carlson BM, Stahl BA. PLoS One. 2013;8(2):e55659. doi:10.1371/journal.pone.0055659.

Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family
Adedipe, F., Grubbs, N., Coates, B. et al. BMC Genomics 20, 899 (2019). doi:10.1186/s12864-019-6218-8

Transcriptome Sequencing of Immature Ants Reveals the Complete Genome Sequence of a New Isolate of Solenopsis invicta Virus 2 from the Mississippi Delta
Margaret L. Allen. Microbiology Resource Announcements May 2019, 8 (18) e01115-18; DOI: 10.1128/MRA.01115-18.

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