SoftGenetics - Software PowerTools for Genetic Analysis

 

 

 

 

 

Using Unique Molecular Identifiers (UMIs) to Remove PCR Duplicates provides increased accuracy

NextGENe software’s Sequence Operation Tool includes the ability to remove PCR duplicates using unique molecular identifiers (UMIs) such as those used by NEBNext Direct or HaloPlex chemistries. The removal of PCR duplicates provides increased accuracy in determining allele frequencies for improved variant calling. The UMIs are random sequences of bases that are used to tag each molecule (fragment) of DNA prior to library amplification, which aids in the identification of PCR duplicates. Illumina instruments generate an I2 Index File for paired-end runs, and an I2 Index file can store these UMIs.


The tool uses UMIs within the Illumina I2 files to identify the PCR duplicates. NextGENe software identifies all the read pairs that share the same UMI, verifies that the template is a duplicate, and retains only the pair that has the highest total quality to be processed along with unique paired reads, while duplicate reads are removed from further processing.

 

Figure 1: NextGENe’s Sequence Operation Tool can be used to remove PCR duplicates using UMIs from an I2 index file.

 

Automation of the duplicate removal using UMIs is easily accomplished by using the NextGENe AutoRun Tool to create a template containing the required analysis specifications.


The duplicate removal settings can be saved by clicking "Save" in the Sequence Operations Tool as shown in Figure 1 above. This settings file can then be loaded in the NextGENe AutoRun Tool’s Job Editor by clicking "Add" next to "Preprocesses". After also loading settings files for any other preprocessing steps needed, such as format conversion and adapter trimming, and for the Process & report settings, a template for the settings can be saved by clicking the "Save" button next to the "Template" field.

 

 

Figure 2: The NextGENe AutoRun Tool can be used to 1) add preprocessing steps including removal of PCR duplicates, 2) select the settings for processing of the sample, and 3) create a template to facilitate quick and easy project set-up for batch analysis.


Projects can then be configured using the template by simply selecting the template and loading the sample files.

 

Download Application Note:

NEBNext Direct Analysis using Unique Molecular IDs (UMIs)

 

Webinars:

Creating Sequence Alignment Projects with NextGENe (view on )

Creating Projects with the NextGENe Software AutoRun Tool (view on )

 

Pricing & Trial Version:
Request 30-day trial/Price Quote

 

Reference Material:
Download/View NextGENe® Brochure
NextGENe User Manual
Annotated Reference Genomes

 

Trademarks property of their respective owners

SoftGenetics - Software PowerTools for Genetic Analysis

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

SOFTWARE


Review all of our software products

 

 

 

 

 

 

 

 

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

 

SoftGenetics Software PowerTools for Genetic Analysis provides current up-to-date information and pricing on all products.
All requests are secure.

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

EXPERTISE


Request trial versions of our software and tap into our knowledge base

 

 

Trial Software

All of our software products are available for review and trial periods. Please use link to request a trial version.

 

Request Trial >>

 

Online Training

Our software professionals are available to you for online training of any of our products. Please contact an expert now.

 

Request Training >>

 

Webinars

SoftGenetics provides online webinars to assist you in the growing knowledge of our products. Visit our Analysis Corner.

 

View Webinars >>

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

SEND US A MESSAGE


Representatives are always ready to assist you


Name *
Email *
Phone

###
-
###
-
####
Message *

 

SoftGenetics - Software PowerTools for Genetic Analysis

100 Oakwood Avenue | Suite 350 | State College, PA 16803 | USA
Phone: 814-237-9340 or 888-791-1270
Email: info@softgenetics.com

 

© 2020 SoftGenetics, LLC. All rights reserved

Trademarks are property of their respective owners

Research use only (RUO)

 

Web design by Lovett Creations