Cogent NGS Immune Profiler Software

Version 2.1.4

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	MaxiSeq Human FFPE TCR+BCR (with UMIs)	634386, 634387
Human TCR	SMART-Seq Human TCR (with UMIs)	634779, 634780 & 634781
	SMARTer Human TCR a/b Profiling Kit v2	634478 & 634479
	MaxiSeq Human FFPE TCR+BCR (with UMIs)	634386, 634387
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 2.1.4 to access full technical support from our dedicated bioinformatics team.

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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 v2.1.4	2025-10-23	Modified Immune Viewer report with “clonal_type” field matching TRUST4-based clonal type assignment Improved sorting of report contents Updated test datasets and added new test dataset for MaxiSeq Human FFPE TCR+BCR (with UMIs) New kit data input options: MaxiSeq Human FFPE TCR+BCR (with UMIs)
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.

Featured products

MaxiSeq Human FFPE TCR+BCR (with UMIs)

Prepare NGS libraries for both human TCR and BCR from 200 ng–1 µg of FFPE RNA with UMI-powered accuracy.

SMART-Seq Human TCR (with UMIs)

SMART-Seq Human TCR (with UMIs) has optimized chemistry, UMIs, and UDIs for more accurate, reliable clonotype calling and quantification.

SMART-Seq Human BCR (with UMIs)

Profile the complete human BCR repertoire with SMART-Seq Human BCR (with UMIs).

SMART-Seq Mouse BCR (with UMIs)

Obtain senstive and reproducible TCR profiling from your mouse models with SMART-Seq Mouse TCR (with UMIs).

SMART-Seq Mouse TCR (with UMIs)

Get senstive and reproducible TCR profiling from your mouse models with SMART-Seq Mouse TCR (with UMIs).

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