Cogent NGS Analysis Pipeline

Version 1.0

Overview

Cogent™ NGS Analysis Pipeline (also referred to as CogentAP) takes input data from sequencing and the well-list file generated by the CellSelect Software (or a well-list-like file generated by a user) and outputs an HTML report and other files, such as a gene matrix, to continue further analysis. R data objects are also output, which can be used as input for Cogent NGS Discovery Software.

After installing, the software consists of the following features:

CogentAP GUI launcher
Command-line interface program
Mini-dataset files (WellList.txt and FASTQ files)—can be used to test the CogentAP functionality
Sample output reports and stats—compare to the analysis results of the mini-dataset test

Sign up to get the Cogent NGS Analysis Pipeline

If you are interested in using CogentAP, 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. You will be emailed a code to activate it. Installation instructions can be found in Cogent NGS Analysis Pipeline v1.0 User Manual and Quick Start Guide.

Supported operating systems

CogentAP can be installed on the following versions of Linux:

CentOS
Ubuntu
RedHat

Hardware requirements

For analyzing Illumina NextSeq® High-Output data:

24-core CPU
64 GB+ RAM
500 GB+ available hard drive space

Analyzing MiniSeq™ or MiSeq® data may be possible on servers with less computational power than the specifications above. Analysis of HiSeq® or NovaSeq™ data would require better hardware than is listed.

Additional third-party software dependencies*

Conda (or Miniconda3)
bcl2fastq conversion software

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

Additional product information

For use in conjunction with workflows on the ICELL8 cx Single-Cell System, ICELL8 Single-Cell System, or select Takara Bio UMI kits. More information is available in the Cogent NGS Analysis Pipeline v1.0 User Manual and Quick Start Guide.

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