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This is the development version of crisprBwa; for the stable release version, see crisprBwa.

BWA-based alignment of CRISPR gRNA spacer sequences

Bioconductor version: Development (3.19)

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

Author: Jean-Philippe Fortin [aut, cre]

Maintainer: Jean-Philippe Fortin <fortin946 at>

Citation (from within R, enter citation("crisprBwa")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to crisprBwa HTML R Script
Reference Manual PDF


biocViews Alignment, CRISPR, FunctionalGenomics, Software
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends methods
Imports BiocGenerics, BSgenome, crisprBase(>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils
System Requirements
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Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
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Depends On Me
Imports Me
Suggests Me crisprDesign
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Follow Installation instructions to use this package in your R session.

Source Package crisprBwa_1.7.0.tar.gz
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macOS Binary (x86_64) crisprBwa_1.7.0.tgz
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Source Repository (Developer Access) git clone
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