nf-core/crisprseq

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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`).

Stars: 63
Forks: 39
Open beginner issues: 0
Indexed issues: 28

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

28 open issues indexed

Add construct-aware paired-guide decoding to the screening workflow Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 28/100

nf-core/crisprseq#278 · Opened Aug 3, 2026
An error occurred when running the plotter.R script Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/crisprseq#275 · 1 comment · Opened Jun 22, 2026
Lack of determinism in results across identical runs Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/crisprseq#269 · 3 comments · Opened Feb 11, 2026
change in BAGEL2 fold-change calculation between crisprseq v2.3.0 and v2.4.0dev Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/crisprseq#265 · Opened Jan 28, 2026
bowtie/align inconsistencies with latest NF version Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/crisprseq#264 · Opened Nov 20, 2025
Add details for samples sheet creation Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/crisprseq#250 · 3 comments · Opened Jun 18, 2025
More than one target per sample Open

enhancement feature-request

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#245 · Opened May 5, 2025
Add 2FAST2Q as an alternative to the MAGeCK count / Bowtie2 combo on the screening workflow Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#243 · 4 comments · Opened Mar 31, 2025
JSON schema: Crisprseq Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/crisprseq#242 · Opened Mar 25, 2025
fastq concatenation Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/crisprseq#241 · Opened Mar 24, 2025
add test for bowtie alignment Open

enhancement

nf-core/crisprseq#240 · 1 assignee · Opened Mar 24, 2025
Allele frequencies for indels and edits Open

enhancement feature-request

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/crisprseq#217 · Opened Nov 15, 2024
Pass DRUGZ in conda Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#189 · Opened Aug 1, 2024
Sample not being detected as edited despite evidence of editing in the bam file Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/crisprseq#188 · 1 comment · Opened Jul 25, 2024
MAGECK mle cnv correction doesn't work Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/crisprseq#179 · 4 comments · Opened Jul 22, 2024
Suggested addition: a PCA illustrating sample/condition/replicates Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/crisprseq#166 · Opened Jul 5, 2024
ZeroDivisionError at alignment_summary.py stage due to low read number in input: mapped_reads_percentage = mapped_reads_count * 100 / total_reads_count Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

nf-core/crisprseq#164 · Opened Jul 4, 2024
N characters introduced into *indels.csv Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 32/100

nf-core/crisprseq#162 · 7 comments · Opened Jul 4, 2024
Pass BAGEL2 in conda Open

enhancement

nf-core/crisprseq#155 · 1 assignee · Opened Jun 14, 2024
Add separate R scripts for local modules Open

enhancement

nf-core/crisprseq#154 · 1 assignee · Opened Jun 14, 2024
Integrate Chronos for screen data Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#112 · 2 comments · Opened Feb 2, 2024
Pass file to cutadapt Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/crisprseq#107 · 2 comments · Opened Jan 17, 2024
Update nf-core/modules/mageck/count Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/crisprseq#88 · Opened Nov 13, 2023
UMI steps to subworkflows Open

enhancement good-first-issue

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/crisprseq#46 · Opened Jun 27, 2023
Alignment subworkflows Open

enhancement good-first-issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/crisprseq#20 · Opened Mar 10, 2023
Reduce cigar parser R script Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#18 · Opened Mar 10, 2023
Add mock samples Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#17 · Opened Mar 10, 2023
Add spikes functionality Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/crisprseq#15 · Opened Mar 10, 2023

nf-core/crisprseq

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