nf-core/crisprseq data

This repository contains the scripts and data used in the nf-core/crisprseq publication.

Benchmarking of resources

benchmarking_results/: Contains tables of resources of different runs with nf-core/crisprseq (crisprseq_full) and CRISPR-Analytics (crispra_full). Contains tables of analysis results run with nf-core/crisprseq (crisprseq_spikes). The tables are obtained from the MultiQC process, which summarises the results. Samples from two projects were analysed, Connelly JP et.al. (2019) (crisp.py) and Sanvicente-García M et.al. (2023) (crispr-A).
crisprseq_vs_crispra.R: R script used to calculate the average run time and CPU hours of both workflows.
spikein_benchmarking.R: R script used to plot a comparison of indels detected in spike-in samples with nf-core/crisprseq and compared with the original publications which analysed the data with crisp.py and CRISPR-A.
public_data/: Contains the projects from the European Nucleotide Archive (ENA) repository filtered by the keyword crispr.
analysis_public_data.R: R script used to classify public available projects into different categories, calculate the percentages and plot them.

Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
benchmarking_results		benchmarking_results
public_data		public_data
LICENSE		LICENSE
README.md		README.md
analysis_percentage_dna-only.png		analysis_percentage_dna-only.png
analysis_public_data.R		analysis_public_data.R
crisprseq_vs_crispra.R		crisprseq_vs_crispra.R
expected_vs_detected_analysis_pipeline.png		expected_vs_detected_analysis_pipeline.png
expected_vs_detected_analysis_pipeline_allsamples.png		expected_vs_detected_analysis_pipeline_allsamples.png
spikein_benchmarking.R		spikein_benchmarking.R