ICELL8 scTCR Analyzer

Overview

The ICELL8 scTCR Analyzer software is for use in conjunction with human TCR a/b profiling on ICELL8 single-cell systems. With identification information derived from the ICELL8 CellSelect imaging software of the ICELL8 systems and FASTQ files generated by Illumina MiSeq®, the analyzer outputs per-well data in a two-step procedure. During its run, the analyzer:

• Aligns reads to reference V, D, J, and C gene segments of the T-cell receptor
• Assembles the aligned reads to extract the CDR3 gene region
• Generates a whole-chip clonotype summary report
• Applies quality control by filtering out clonotypes with relatively poor quality based on the readings from negative controls included on the chip

The analyzer reports filtering statistics, produces tables extracting the top three clonotypes, and generates files that can be used as input for data visualization, such as a VJ join chord diagram.

Upon acceptance of the EULA and submitting the form, your browser will be directed to a website where you can download the ICELL8 scTCR Analyzer Software. You will access the software as a zip archive containing the following files:

• Analyzer GUI launcher (Windows and MacOS only)
• Command-line interface program (Windows, MacOS, or Linux)
• Example data files—can be used to test the Analyzer functionality (WellList.txt and FASTQ files)
• Sample output—compare to the analysis results of the example data

Supported operating systems

• Windows 7, Windows 10
• Linux (Centos 6, Centos 7)
• Mac OS X El Capitan (version 10.11 and up)

Hardware requirements

• 16 GB RAM
• 100 GB available hard drive space

Additional third-party software dependencies*

• Java 1.7 or higher
• Python 3.6 or higher
• MiXCR 2.1.8

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

Additional product information

For use only in conjunction with workflows on the ICELL8 cx Single-Cell System or ICELL8 Single-Cell System. More information is available in the ICELL8 scTCR Analyzer User Guide.