QUANTS is a bioinformatics best-practice pipeline for the conversion of FASTQ, generated by saturation genome editing (SGE) screens, into counts.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

• Nextflow (>=21.10.6)

• Docker or Singularity.

The QUANTS pipeline comes with documentation about the pipeline usage, input, parameters and output.

QUANTS was originally written by Victoria Offord using the foundation provided by nf-core.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.