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Cogent NGS Analysis Pipeline
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.
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
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 v1.5.1 User Manual and Quick Start Guide.
Cogent NGS Analysis Pipeline version history
|Version number||Release date||Notes|
|mappa Analyzer 1.0||2019-06-07|
Scale your biomarker discovery with full-transcriptome scRNA-seq
SMART-Seq Pro Application Kit - 2 Chip
- Capture critical insights—identify gene fusions, splice variants, and SNPs that end-counting technologies can miss
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- Prepare libraries with ease—automate your workflow from sample to library prep to analysis
- Get clear results—simplify your bioinformatics analysis with integrated Cogent NGS tools
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