@@ 21322,6 21322,47 @@ on marker set compatibility, similarity in genomic characteristics, and
proximity within a reference genome.")
(license license:gpl3+)))
+(define-public chromap
+ (package
+ (name "chromap")
+ (version "0.2.7")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/haowenz/chromap")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "099y3kac6npiqyx5prc9ggigw6248j7kchjznqvd9hxkq24rrsqs"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda _
+ (install-file "chromap" (string-append #$output "/bin")))))))
+ (inputs (list zlib))
+ (home-page "https://github.com/haowenz/chromap")
+ (synopsis "Fast alignment and preprocessing of chromatin profiles")
+ (description "Chromap is a fast method for aligning and preprocessing high
+throughput chromatin profiles. Typical use cases include:
+
+@itemize
+@item trimming sequencing adapters, mapping bulk ATAC-seq or ChIP-seq genomic
+ reads to the human genome and removing duplicates;
+@item trimming sequencing adapters, mapping single cell ATAC-seq genomic reads
+ to the human genome, correcting barcodes, removing duplicates and performing
+ Tn5 shift;
+@item split alignment of Hi-C reads against a reference genome.
+@end itemize")
+ (supported-systems '("x86_64-linux")) ;requires CPU with SSE4.1
+ (license license:expat)))
+
(define-public umi-tools
(package
(name "umi-tools")