Cogent™ NGS Immune Profiler Software

Version 2.0

Overview

Cogent NGS Immune Profiler (CogentIP) is software designed to analyze sequence data stored in FASTQ files generated by Illumina sequencers from libraries prepared using certain Takara Bio immune profiling kits. After analyzing sequence data, the output CSV file can be uploaded to our web-based Cogent NGS Immune Viewer to quickly visualize immune profiling data and generate publication-ready figures.

The Immune Profiler software is free to use and recommended for use with the following immune profiling kits:

Species & repertoire type	Kit name	Cat. #
Human BCR	SMART-Seq Human BCR (with UMIs)	634776, 634777 & 634778
Human BCR	SMARTer Human BCR IgG IgM H/K/L Profiling Kit	634466 & 634467
Human TCR	SMART-Seq Human TCR (with UMIs)	634779, 634780 & 634781
Human TCR	SMARTer Human TCR a/b Profiling Kit v2	634478 & 634479
Mouse BCR	SMART-Seq Mouse BCR (with UMIs)	634351, 634352 & 634353
Mouse TCR	SMART-Seq Mouse TCR (with UMIs)	634814, 634815 & 634816
Mouse TCR	SMARTer Mouse TCR a/b Profiling Kit	634403 & 634404

After installing, the software consists of the following features:

Command-line interface program
Files that can be used to install Nextflow—required third-party software
Mini-dataset files (FASTQ and metadata CSV files)—used to test the CogentIP functionality
Sample output result files—used to compare to your results of the mini-dataset test

For more information, see the Cogent NGS Immune Profiler User Manual.

NOTE: CogentIP v1.0–1.6.1 is no longer supported by Takara Bio. Please upgrade to Version 2.0 to access full technical support from our dedicated bioinformatics team.

Cat. #	Product	Size	Price	License	Quantity	Details
650005.V3.1	Cogent™ NGS Analysis Pipeline	Each	Inquire for Quotation		*
Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

*You must be logged in to a Purchasing Account in order to purchase these products online, since the purchase of these products may be restricted depending on your account type. Researchers at not-for-profit accounts receive a limited use license with their purchase of the product. Researchers at for-profit accounts must obtain a license prior to purchase. For details please contact licensing@takarabio.com.

More Information

Supported operating systems

OS X (El Capitan v10.11 and up)
CentOS 6 or higher, RedHat 7.5 or higher

Hardware requirements

16 GB RAM
At least 100 GB of available hard drive space (dependent on input FASTQ file size)

Additional third-party software dependencies*

Java 11 (Java SE 11)
Python 3.6 or higher
conda 23.7.4 or higher

Not included with the software; must be downloaded and installed separately.

Additional product information

For use in conjunction with the products in the table above.

More information is available in the Cogent NGS Immune Profiler User Manual, or a streamlined protocol can be found in the Cogent NGS Immune Profiler and Cogent NGS Immune Viewer Quick Start Guide.

Cogent NGS Immune Profiler Software version history
Version number	Release date	Notes
Cogent NGS Immune Profiler v2.0	2024-11-18	Updated third-party software implementation—replaced previous third-party tools with TRUST4 immune profiling algorithm New kit data input options: SMART-Seq Mouse BCR (with UMIs) SMARTer Human TCR a/b Profiling Kit (legacy kit) SMARTer Mouse TCR a/b Profiling Kit (legacy kit) Improved algorithms for linker correction and isotype-specific primer detection Improved handling of large FASTQ files Customizable usage control of server CPU resources while running the pipeline
Cogent NGS Immune Profiler v1.6.1	2023-11-17	Updated third-party software implementation New download procedure (documentation-only)
Cogent NGS Immune Profiler v1.6	2023-09-01	New kit data input option: SMART-Seq Mouse TCR (with UMIs)
Cogent NGS Immune Profiler v1.5	2022-10-07	New kit data input options: SMART-Seq Human BCR (with UMIs) SMART-Seq Human TCR (with UMIs) Additional set of output files compliant with Adaptive Immune Receptor Repertoire (AIRR) Community standards Single installation package—compatible with both Linux and MacOS
Cogent NGS Immune Profiler v1.0	2020-08-04	Kit data input options: SMARTer Human BCR IgG IgM H/K/L Profiling Kit, SMARTer Human TCR a/b Profiling Kit v2

Sign up to get Cogent NGS Immune Profiler Software

If you are interested in using the Cogent NGS Immune Profiler, please review the End User License Agreement (EULA) before populating the required fields of the form.

After checking the box to indicate acceptance of the EULA and submitting the completed form, your browser will be directed to a page where you can download the software. Installation instructions can be found in Cogent NGS Immune Profiler User Manual and Quick Start Guide.

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