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nf-core/crisprseq data

DOI

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.
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