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PIPseeker Software for Data Analysis

  • Analyze sequencing data from PIPseq™ 3′ Single Cell Gene Expression libraries
  • Obtain summary metrics, diagnostic plots, clustering and differential gene expression tables
  • Generate standard feature-barcode count matrices compatible with standard tertiary analysis packages
  • Compatible with Windows, MacOS, and Linux

Pipeline Overview

PIPseeker provides a complete analysis solution for PIPseq samples. The input to PIPseeker is a set of demultiplexed FASTQ files. The workflow is comprised of the following steps:

  1. FASTQ processing, including barcode matching, quality control and (optionally) downsampling
  2. Mapping with STAR aligner
  3. Parsing of the STAR output
  4. UMI deduplication and counting
  5. Cell calling
  6. Clustering
  7. Differential expression
  8. Metrics extraction
  9. Report generation

System Requirements 

  • PIPseeker can run on Windows, macOS and Linux operating systems.
  • The recommended hardware specifications are 64 GB of RAM and 1TB hard disk space.
  • To ensure compatibility with as many operating system versions and distributions as possible, PIPseeker runs from a Docker container and requires a local installation of Docker
  • PIPseeker has been tested on Ubuntu 18.04 and 20.04, Windows 10 and macOS 12.3.1


PIPseeker is available for download as a compressed, self-contained package. Common reference packages are also provided here for convenience, but users can generate their own references as needed.

PIPseeker User Guide (PDF)