Cogent NGS Analysis Pipeline
Version 1.5.1
Overview
Cogent™ NGS Analysis Pipeline (also referred to as CogentAP) is bioinformatic software for user-friendly alignment and mapping of sequencing data generated with Takara Bio platforms. CogentAP inputs raw sequencing data and a well-list file (generated by the ICELL8 Single-Cell System’s CellSelect Software or a similar user-generated file) and outputs an HTML report and other files, such as a gene matrix, to continue further analysis. Output also includes R data objects, which may be used as input for Cogent NGS Discovery Software.
Example output available in the CogentAP HTML report.
After installing, the software consists of the following features:
- CogentAP GUI launcher
- Command-line interface program
- Mini-dataset files (WellList.txt and FASTQ files)—used to test the CogentAP functionality
- Sample output reports and stats—used to compare to the analysis results of the mini-dataset test
Supported operating systems
CogentAP can be installed on the following versions of Linux:
- CentOS 6.9 & 6.10
- RedHat 7.5
- Ubuntu 17
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.
Supported applications
See a list of supported applications.
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 v1.5.1 User Manual and Quick Start Guide.
Cogent NGS Analysis Pipeline version history
Version number | Release date | Notes |
---|---|---|
CogentAP 1.5.1 | 2022-03-25 |
|
CogentAP 1.5 | 2021-12-03 |
|
CogentAP 1.0 | 2020-09-11 |
|
mappa Analyzer 1.0 | 2019-06-07 |
|

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