aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--gnu/packages/bioinformatics.scm34
1 files changed, 34 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92c0692f45..9b819d1a23 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15247,6 +15247,40 @@ database. That database maps k-mers to the lowest common ancestor (LCA) of all
genomes known to contain a given k-mer.")
(license license:expat)))
+(define-public lofreq
+ (package
+ (name "lofreq")
+ (version "2.1.5")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/CSB5/lofreq")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0qssrn3mgjak7df6iqc1rljqd3g3a5syvg0lsv4vds43s3fq23bl"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:test-target "bug-tests"
+ #:tests? #false)) ; test data are not included
+ (inputs
+ `(("htslib" ,htslib)
+ ("python" ,python-wrapper)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("which" ,which)))
+ (home-page "https://csb5.github.io/lofreq/")
+ (synopsis "Sensitive variant calling from sequencing data ")
+ (description "LoFreq is a fast and sensitive variant-caller for inferring
+SNVs and indels from next-generation sequencing data. It makes full use of
+base-call qualities and other sources of errors inherent in
+sequencing (e.g. mapping or base/indel alignment uncertainty), which are
+usually ignored by other methods or only used for filtering.")
+ (license license:expat)))
+
(define-public python-pyliftover
(package
(name "python-pyliftover")