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| author | Yuri Victorovich <yuri@FreeBSD.org> | 2023-07-11 01:44:10 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2023-07-11 01:44:34 +0000 |
| commit | 2512450302863b1bcfc8f3b3dc216b1ec64091c1 (patch) | |
| tree | 387b317d27dc0ee9d7b8644d1cda298503ffafac /biology | |
| parent | 86cf72ac83e63993e7e6ac23954585a885b7922e (diff) | |
| download | ports-2512450302863b1bcfc8f3b3dc216b1ec64091c1.tar.gz ports-2512450302863b1bcfc8f3b3dc216b1ec64091c1.zip | |
biology/mashmap: New port: Fast approximate aligner for long DNA sequences
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/mashmap/Makefile | 24 | ||||
| -rw-r--r-- | biology/mashmap/distinfo | 3 | ||||
| -rw-r--r-- | biology/mashmap/pkg-descr | 11 |
4 files changed, 39 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index fe34cafefca7..71d625b98e9f 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -97,6 +97,7 @@ SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 + SUBDIR += mashmap SUBDIR += megahit SUBDIR += metaeuk SUBDIR += migrate diff --git a/biology/mashmap/Makefile b/biology/mashmap/Makefile new file mode 100644 index 000000000000..d9dc5f5fafa4 --- /dev/null +++ b/biology/mashmap/Makefile @@ -0,0 +1,24 @@ +PORTNAME= mashmap +DISTVERSIONPREFIX= v +DISTVERSION= 3.0.6 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Fast approximate aligner for long DNA sequences +WWW= https://github.com/marbl/MashMap + +LICENSE= PD +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +LIB_DEPENDS= libgsl.so:math/gsl + +USES= cmake compiler:c++17-lang localbase:ldflags + +USE_GITHUB= yes +GH_ACCOUNT= marbl +GH_PROJECT= MashMap + +PLIST_FILES= bin/mashmap \ + bin/mashmap-align + +.include <bsd.port.mk> diff --git a/biology/mashmap/distinfo b/biology/mashmap/distinfo new file mode 100644 index 000000000000..7cbf1e62148e --- /dev/null +++ b/biology/mashmap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1689039441 +SHA256 (marbl-MashMap-v3.0.6_GH0.tar.gz) = 53d1b4efad6650d8efbc28325637d1bdacd108eaad70fcc28e927f40ac5c2112 +SIZE (marbl-MashMap-v3.0.6_GH0.tar.gz) = 234093 diff --git a/biology/mashmap/pkg-descr b/biology/mashmap/pkg-descr new file mode 100644 index 000000000000..4460733166d2 --- /dev/null +++ b/biology/mashmap/pkg-descr @@ -0,0 +1,11 @@ +MashMap implements a fast and approximate algorithm for computing local +alignment boundaries between long DNA sequences. It can be useful for mapping +genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a +minimum alignment length and an identity threshold for the desired local +alignments, Mashmap computes alignment boundaries and identity estimates using +k-mers. It does not compute the alignments explicitly, but rather estimates an +unbiased k-mer based Jaccard similarity using a combination of minmers (a novel +winnowing scheme) and MinHash. This is then converted to an estimate of sequence +identity using the Mash distance. An appropriate k-mer sampling rate is +automatically determined using the given minimum local alignment length and +identity thresholds. |