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:
- FASTQ processing, including barcode matching, quality control and (optionally) downsampling
- Mapping with STAR aligner
- Parsing of the STAR output
- UMI deduplication and counting
- Cell calling
- Differential expression
- Metrics extraction
- Report generation
- 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.