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.


Name Date Download
1 PoolQ Version 3.11.0 15 February 2024 zip
2 PoolQ Version 3.11.0 Manual 15 February 2024 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

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: My data has been generated and is in a format as recommended by the Genetic Perturbation Platform. Is there a simple protocol that I can follow to help me run PoolQ and interpret its results?

Provided you have consulted our platform prior to your experiment and are confident that your data is compatible with our standard sequence protocols, you may find the "Pooled Screening Deconvolution Using PoolQ" document found in the protocol section of our site to be useful in addition to the PoolQ Manual.

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.