nf-core/crisprseq
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (targeted
) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (screening
).
crisprcrispr-analysiscrispr-casngs
Version history
v2.0.0 - Paprika Lovelace - [05.07.2023]
Highlights 🌟
This release includes a whole new analysis type : functional genomics screenings (activation, interference or knock outs screens). For CRISPR-targeting, UMIs clustering is now supported.
The usage of the pipeline now includes the flag --analysis
<screening,targeted> to allow the user to indicate which analysis they would like to run.
Added ➕
- Crisprseq screening analysis : mageck mle, mageck rra, mageck count and crisprcleanr-normalize (#22)
- Add new parameter
--analysis
to select analysis type (screening/targeted) (#27) - Tests to run screening analysis (#926)
- Metro map for targeted analysis (#35)
- Add new parameters
--reference
and--protospacer
(#45) - Add UMI clustering to crisprseq-targeted (#24)
- Template update v2.8 (#21)
Fixed 🧰
Initial release of nf-core/crisprseq, created with the nf-core template.