Cogent NGS Analysis Pipeline
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
Supported operating systems
CogentAP can be installed on the following versions of Linux:
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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