CRISPR-detector

Here we propose our CRISPR-detector to facilitate the CRISPR-edited amplicon and whole genome sequencing data analysis, with functions that existing tools are not able to provide.

CRISPR-detector brings the following four key innovations :

1. optimized processing time allowing for hundreds of amplicons or whole genome sequencing data;
2. integrated structural variation calling;
3. edited and control sample co-analysis, to remove background variants not induced by gene-editing;
4. functional and clinical consequences annotation of editing-induced mutations.

System requirements

Sentieon module

Download sentieon toolkit from https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-202010.03.tar.gz
You may request a license by sending emails to [email protected]

export SENTIEON_LICENSE=PATH_TO_SENTIEON/sentieon-genomics-202010.03/localhost_eval.lic
export PATH=PATH_TO_SENTIEON/sentieon-genomics-202010.03/bin:$PATH

Python packages

pip install biopython
pip install pyfaidx
pip install -U textwrap3
conda install blast
conda install samtools

ANNOVAR

Download ANNOVAR from https://www.openbioinformatics.org/annovar/annovar_download_form.php

perl annotate_variation.pl -downdb -webfrom annovar avdblist humandb/ -buildver hg38
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar clinvar_20210501 humandb/
export PATH=PATH_TO_ANNOVAR/annovar:$PATH

Organism Homo sapiens Experiment type sequencing data support variant annotations from refGene & ClinVar, other species may only support refGene annotations

Usage

1. Single amplicon & pooled amplicons sequencing data analysis

python CRISPRdetectorCORE.py
--sample, sample name & output dir
--e1, treated group fq1 path, required = True
--e2, treated group fq2 path, required = False
--c1, control group fq2 path, required = False
--c2, control group fq2 path, required = False
--ref_fasta, single or pooled amplicon(s) sequence(s) path in fasta format, required=True
--threads, number of threads to run sentieon minimap2 & driver module, default=1
--anno, annotate variants with ANNOVAR [1] or not run ANNOVAR [2], required=False
--assembly, path to assembly in fasta format : hg38.fa mm9.fa ... required=False
--species, species : Homo_sapiens,Mus_musculus... required=False
--db, ANNOVAR database path, required=False

2. Whole genome sequencing (WGS) data analysis

python CRISPRdetectorWGS.py
--e1, treated group fq1 path, required = True
--e2, treated group fq2 path, required = False
--c1, control group fq2 path, required = False
--c2, control group fq2 path, required = False
--sample, sample name & output dir
--threads, number of threads to run sentieon minimap2 & driver module, default=1
--bed, bed format file input to call variants of interest region, required=False
--anno, annotate variants with ANNOVAR [1] or not run ANNOVAR [2], required=False
--assembly, path to assembly in fasta format : hg38.fa mm9.fa ... required=False
--species, species : Homo_sapiens,Mus_musculus... required=False
--db, ANNOVAR database path, required=False