Cogent NGS Analysis Pipeline

Cogent NGS Analysis Pipeline (CogentAP) is bioinformatics software for analyzing RNA-seq NGS data generated using the following systems or kits.

• ICELL8 cx Single-Cell System or the ICELL8 Single-Cell system on the single-cell full-length transcriptome or single-cell differential expression (3' DE or 5' DE) workflows, including 3′ DE for UMI.
• SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Pico v3)

The program takes input files from sequencers and outputs an HTML report, with results typical to single-cell analysis, and other files, such as a gene matrix, to continue further analysis. An R data object with results computed based on recommended parameters is also created. Either the standard output files or the R data object can serve as input for Cogent NGS Discovery Software.