diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 354 |
1 files changed, 307 insertions, 47 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc182fbea3..d37d93047e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com> +;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1615,14 +1616,14 @@ gapped, local, and paired-end alignment modes.") (define-public bowtie1 (package (name "bowtie1") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" - version "/bowtie-src-x86_64.zip")) + version "/bowtie-" version "-src.zip")) (sha256 (base32 - "0vmiqdhc9dzyfy9sh6vgi7k9xy2hiw8g87vbamnc6cgpm179zsa4")) + "11dbihdnrizc6qhx9xsw77w3q5ssx642alaqzvhxx32ak9glvq04")) (modules '((guix build utils))) (snippet '(substitute* "Makefile" @@ -1633,7 +1634,7 @@ gapped, local, and paired-end alignment modes.") (arguments '(#:tests? #f ; no "check" target #:make-flags - (list "all" + (list "CC=gcc" "all" (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases @@ -3819,7 +3820,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (define-public hmmer (package (name "hmmer") - (version "3.2.1") + (version "3.3.2") (source (origin (method url-fetch) @@ -3827,9 +3828,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) (sha256 (base32 - "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) + "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl))) + (native-inputs `(("perl" ,perl) + ("python" ,python))) ; for tests (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description @@ -6730,7 +6732,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.7.3a") + (version "2.7.8a") (source (origin (method git-fetch) (uri (git-reference @@ -6739,7 +6741,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (file-name (git-file-name name version)) (sha256 (base32 - "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq")) + "0zc5biymja9zml9yizcj1h68fq9c6sxfcav8a0lbgvgsm44rvans")) (modules '((guix build utils))) (snippet '(begin @@ -6815,6 +6817,32 @@ sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) +(define-public star-for-pigx + (package + (inherit star) + (name "star") + (version "2.7.3a") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/alexdobin/STAR") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "source/Makefile" + (("/bin/rm") "rm")) + ;; Remove pre-built binaries and bundled htslib sources. + (delete-file-recursively "bin/MacOSX_x86_64") + (delete-file-recursively "bin/Linux_x86_64") + (delete-file-recursively "bin/Linux_x86_64_static") + (delete-file-recursively "source/htslib") + #t)))))) + (define-public starlong (package (inherit star) (name "starlong") @@ -7054,14 +7082,14 @@ data in the form of VCF files.") (define-public infernal (package (name "infernal") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (string-append "http://eddylab.org/software/infernal/" "infernal-" version ".tar.gz")) (sha256 (base32 - "0pm8bm3s6nfa0av4x6m6h27lsg12b3lz3jm0fyh1mc77l2isd61v")))) + "1z4mgwqg1j4n5ika08ai8mg9yjyjhf4821jp83v2bgwzxrykqjgr")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) @@ -7129,6 +7157,55 @@ clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.") (license license:gpl3))) +(define-public r-archr + (let ((commit "46b519ffb6f73edf132497ac31650d19ef055dc1") + (revision "1")) + (package + (name "r-archr") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GreenleafLab/ArchR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1zj3sdfhgn2q2256fmz61a92vw1wylyck632d7842d6knd0v92v8")))) + (properties `((upstream-name . "ArchR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-chromvar" ,r-chromvar) + ("r-complexheatmap" ,r-complexheatmap) + ("r-data-table" ,r-data-table) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-gtools" ,r-gtools) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-motifmatchr" ,r-motifmatchr) + ("r-nabor" ,r-nabor) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5" ,r-rhdf5) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-uwot" ,r-uwot))) + (home-page "https://github.com/GreenleafLab/ArchR") + (synopsis "Analyze single-cell regulatory chromatin in R") + (description + "This package is designed to streamline scATAC analyses in R.") + (license license:gpl2+)))) + (define-public r-scde (package (name "r-scde") @@ -7237,14 +7314,14 @@ includes software to (define-public r-genefilter (package (name "r-genefilter") - (version "1.72.0") + (version "1.72.1") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633")))) + "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -7403,14 +7480,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44")))) + "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7537,14 +7614,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j")))) + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7702,6 +7779,79 @@ clusters.") (home-page "https://sourceforge.net/projects/pardre/") (license license:gpl3+))) +(define-public ngshmmalign + (package + (name "ngshmmalign") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/cbg-ethz/ngshmmalign/" + "releases/download/" version + "/ngshmmalign-" version ".tar.bz2")) + (sha256 + (base32 + "0jryvlssi2r2ii1dxnx39yk6bh4yqgq010fnxrgfgbaj3ykijlzv")))) + (build-system cmake-build-system) + (arguments '(#:tests? #false)) ; there are none + (inputs + `(("boost" ,boost))) + (home-page "https://github.com/cbg-ethz/ngshmmalign/") + (synopsis "Profile HMM aligner for NGS reads") + (description + "ngshmmalign is a profile HMM aligner for NGS reads designed particularly +for small genomes (such as those of RNA viruses like HIV-1 and HCV) that +experience substantial biological insertions and deletions.") + (license license:gpl2+))) + +(define-public prinseq + (package + (name "prinseq") + (version "0.20.4") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/prinseq/standalone/" + "prinseq-lite-" version ".tar.gz")) + (sha256 + (base32 + "0vxmzvmm67whxrqdaaamwgjk7cf0fzfs5s673jgg00kz7g70splv")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #false ; no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (for-each (lambda (file) + (chmod file #o555) + (install-file file bin) + (wrap-script (string-append bin "/" (basename file)) + `("PERL5LIB" ":" prefix + (,(getenv "PERL5LIB"))))) + (find-files "." "prinseq.*.pl")))))))) + (inputs + `(("guile" ,guile-3.0) ; for wrapper scripts + ("perl" ,perl) + ("perl-cairo" ,perl-cairo) + ("perl-data-dumper" ,perl-data-dumper) + ("perl-digest-md5" ,perl-digest-md5) + ("perl-getopt-long" ,perl-getopt-long) + ("perl-json" ,perl-json) + ("perl-statistics-pca" ,perl-statistics-pca))) + (home-page "http://prinseq.sourceforge.net/") + (synopsis "Preprocess sequence data in FASTA or FASTQ formats") + (description + "PRINSEQ is a bioinformatics tool to help you preprocess your genomic or +metagenomic sequence data in FASTA or FASTQ formats. The tool is written in +Perl and can be helpful if you want to filter, reformat, or trim your sequence +data. It also generates basic statistics for your sequences.") + (license license:gpl3+))) + (define-public ruby-bio-kseq (package (name "ruby-bio-kseq") @@ -7954,13 +8104,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.28.0") + (version "0.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv")))) + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7981,13 +8131,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.24.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b")))) + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -8063,13 +8213,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.32.0") + (version "3.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg")))) + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -8266,13 +8416,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.46.0") + (version "2.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf")))) + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -8401,13 +8551,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.16.0") + (version "0.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g")))) + "1d75zrhha1v7dhbvjp6a4iap441l5k268w0jjxklpqywbqns7l3d")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -9697,13 +9847,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "11pmn191n0ga28x1w20cm2cmw8kddl29q6h2xfjjba5bspp2g613")))) + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -10037,14 +10187,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx")))) + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -10356,14 +10506,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.40.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0xm50wgjjjymv71mbv1clnhx4m12nrd1pc6vfplpdqr5q49v3yd5")))) + "1iawa03dy4bl333my69d4sk7d74cjzfg5dpcxga6q5dglan4sp8r")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10635,6 +10785,72 @@ explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.") (license license:gpl3)))) +(define-public r-cellchat + (let ((commit + "21edd226ca408e4c413408f98562d71ee0b54e5d") + (revision "1")) + (package + (name "r-cellchat") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sqjin/CellChat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cvzl9mi8jjznpql2gv67swnk1dndn3a2h22z5l84h7lwpwjmh53")) + (snippet + '(for-each delete-file '("src/CellChat.so" + "src/CellChat_Rcpp.o" + "src/RcppExports.o"))))) + (properties `((upstream-name . "CellChat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-circlize" ,r-circlize) + ("r-colorspace" ,r-colorspace) + ("r-complexheatmap" ,r-complexheatmap) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-expm" ,r-expm) + ("r-fnn" ,r-fnn) + ("r-forcats" ,r-forcats) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) + ("r-gg-gap" ,r-gg-gap) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-nmf" ,r-nmf) + ("r-patchwork" ,r-patchwork) + ("r-pbapply" ,r-pbapply) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-reshape2" ,r-reshape2) + ("r-reticulate" ,r-reticulate) + ("r-rspectra" ,r-rspectra) + ("r-rtsne" ,r-rtsne) + ("r-scales" ,r-scales) + ("r-shape" ,r-shape) + ("r-sna" ,r-sna) + ("r-stringr" ,r-stringr) + ("r-svglite" ,r-svglite))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/sqjin/CellChat") + (synopsis "Analysis of cell-cell communication from single-cell transcriptomics data") + (description + "This package infers, visualizes and analyzes the cell-cell +communication networks from scRNA-seq data.") + (license license:gpl3)))) + (define-public sambamba (package (name "sambamba") @@ -11201,7 +11417,7 @@ browser.") (inputs `(("perl" ,perl) ("java-commons-cli" ,java-commons-cli))) - (home-page "http://fureylab.web.unc.edu/software/fseq/") + (home-page "https://fureylab.web.unc.edu/software/fseq/") (synopsis "Feature density estimator for high-throughput sequence tags") (description "F-Seq is a software package that generates a continuous tag sequence @@ -11370,7 +11586,7 @@ using nucleotide or amino-acid sequence data.") (define-public kallisto (package (name "kallisto") - (version "0.44.0") + (version "0.46.2") (source (origin (method git-fetch) (uri (git-reference @@ -11379,7 +11595,10 @@ using nucleotide or amino-acid sequence data.") (file-name (git-file-name name version)) (sha256 (base32 - "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m")))) + "0ij5n7v3m90jdfi7sn8nvglfyf58abp1f5xq42r4k73l0lfds6xi")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "ext/htslib/")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no "check" target @@ -11402,7 +11621,7 @@ using nucleotide or amino-acid sequence data.") #t))))) (inputs `(("hdf5" ,hdf5) - ("htslib" ,htslib) + ("htslib" ,htslib-1.9) ("zlib" ,zlib))) (home-page "https://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") @@ -12387,7 +12606,7 @@ once. This package provides tools to perform Drop-seq analyses.") ("snakemake" ,snakemake) ("fastqc" ,fastqc) ("multiqc" ,multiqc) - ("star" ,star) + ("star" ,star-for-pigx) ("trim-galore" ,trim-galore) ("htseq" ,htseq) ("samtools" ,samtools) @@ -12598,7 +12817,7 @@ methylation and segmentation.") ("pandoc-citeproc" ,pandoc-citeproc) ("samtools" ,samtools) ("snakemake" ,snakemake) - ("star" ,star) + ("star" ,star-for-pigx) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) ("r-cowplot" ,r-cowplot) @@ -14045,18 +14264,24 @@ choosing which reads pass the filter.") #t))) (add-after 'install 'wrap-programs (lambda* (#:key outputs #:allow-other-keys) - (for-each (lambda (file) - (wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,path)))) - (find-files "/share/nanopolish/scripts" "\\.py")) - (for-each (lambda (file) - (wrap-program file `("PERL5LIB" ":" prefix (,path)))) - (find-files "/share/nanopolish/scripts" "\\.pl")) - #t))))) + (let ((pythonpath (getenv "GUIX_PYTHONPATH")) + (perl5lib (getenv "PERL5LIB")) + (scripts (string-append (assoc-ref outputs "out") + "/share/nanopolish/scripts"))) + (for-each (lambda (file) + (wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))) + (find-files scripts "\\.py")) + (for-each (lambda (file) + (wrap-script file `("PERL5LIB" ":" prefix (,perl5lib)))) + (find-files scripts "\\.pl")))))))) (inputs - `(("eigen" ,eigen) + `(("guile" ,guile-3.0) ; for wrappers + ("eigen" ,eigen) ("hdf5" ,hdf5) ("htslib" ,htslib) ("perl" ,perl) + ("bioperl" ,bioperl-minimal) + ("perl-getopt-long" ,perl-getopt-long) ("python" ,python-wrapper) ("python-biopython" ,python-biopython) ("python-numpy" ,python-numpy) @@ -15488,6 +15713,41 @@ manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.") (license license:expat)))) +(define-public indelfixer + (package + (name "indelfixer") + (version "1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cbg-ethz/InDelFixer/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10ak05x8i1bx2p7rriv2rglqg1wr7c8wrhjrqlq1wm7ka99w8i79")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "InDelFixer.jar" + #:source-dir "src/main/java" + #:test-dir "src/test")) + (inputs + `(("java-commons-lang2" ,java-commons-lang) + ("java-args4j" ,java-args4j))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "https://github.com/cbg-ethz/InDelFixer/") + (synopsis "Iterative and sensitive NGS sequence aligner") + (description "InDelFixer is a sensitive aligner for 454, Illumina and +PacBio data, employing a full Smith-Waterman alignment against a reference. +This Java command line application aligns Next-Generation Sequencing (NGS) and +third-generation reads to a set of reference sequences, by a prior fast k-mer +matching and removes indels, causing frame shifts. In addition, only a +specific region can be considered. An iterative refinement of the alignment +can be performed, by alignment against the consensus sequence with wobbles. +The output is in SAM format.") + (license license:gpl3+))) + (define-public libsbml (package (name "libsbml") |