PoolQ

Overview

PoolQ is a tool designed to quantify the results of pooled screens based on DNA sequencing data. Using DNA barcodes applied to genomic DNA samples via PCR, PoolQ can separately quantify multiple samples that have been pooled to make maximum use of sequencing depth. PoolQ produces a matrix of read counts corresponding to barcodes from supplied condition and reference files. It supports FASTQ, SAM/BAM, and a simple text sequence format, allowing screeners to use a variety of sequencing technologies without needing to convert file formats.

If you've received a PoolQ data delivery link from GPP, or would like to run PoolQ independently, review our recommended Screen Deconvolution with PoolQ guidance. The PoolQ Manual (linked below) provides more extensive details on the full capabilities and maintenance of the software.

Downloads

Name Date Download
1 PoolQ Version 3.13.2 03 December 2025 zip
2 PoolQ Version 3.13.2 Manual 03 December 2025 pdf
3 PoolQ Version 2.2.0 29 Feb 2016 zip
4 PoolQ Version 2.2.0 Manual 29 Feb 2016 pdf
All PoolQ Versions
Changelog

Frequently Asked Questions

Q: Will PoolQ run on my computer?

PoolQ can run on any computer with a Java runtime environment (Java 8 or greater). However, the PoolQ algorithm is memory-intensive; PoolQ will run best on a computer that has at least 2G of RAM available.

Q: What input file formats does PoolQ support?

PoolQ was designed to run on FASTQ and SAM/BAM formats. However, it is also possible to run PoolQ on a simple text file with each sequencing read on a single line.

Q: Is it possible to get the source code for PoolQ?

Yes, the source code is publicly available under a BSD 3-clause license as of version 3.5.0.

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