subread High-performance read alignment, quantification and mutation discovery

2.0.1 biology =0 2.0.1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2020-06-05 01:55:58

Last Update: 2020-06-05 02:55:49

SVN Revision: 537982

License: GPLv3

Description:

The Subread package comprises a suite of software programs for processing next-gen sequencing read data including: Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants. Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well. featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins. Sublong: a long-read aligner that is designed based on seed-and-vote. exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises. WWW: http://bioinf.wehi.edu.au/subread-package/

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (19 items)

1. /usr/local/share/licenses/subread-2.0.1/catalog.mk
2. /usr/local/share/licenses/subread-2.0.1/LICENSE
3. /usr/local/share/licenses/subread-2.0.1/GPLv3
4. bin/detectionCall
5. bin/exactSNP
6. bin/featureCounts
7. bin/flattenGTF
8. bin/genRandomReads
9. bin/propmapped
10. bin/qualityScores
11. bin/removeDup
12. bin/repair
13. bin/subindel
14. bin/subjunc
15. bin/sublong
16. bin/subread-align
17. bin/subread-buildindex
18. bin/subread-fullscan
19. bin/txUnique

Collapse this list.

Dependency lines:

• subread>0:biology/subread

To install the port: cd /usr/ports/biology/subread/ && make install clean

To add the package: pkg install subread

PKGNAME: subread

Flavors: there is no flavor information for this port.

distinfo:

TIMESTAMP = 1591305316 SHA256 (subread-2.0.1-source.tar.gz) = d808eb5b1823c572cb45a97c95a3c5acb3d8e29aa47ec74e3ca1eb345787c17b SIZE (subread-2.0.1-source.tar.gz) = 23260381

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. gmake>=4.3 : devel/gmake

Library dependencies:

1. libsysinfo.so : devel/libsysinfo

There are no ports dependent upon this port

Configuration Options

No options to configure

USES:

gmake localbase:ldflags

Master Sites:

1. http://downloads.sourceforge.net/project/subread/subread-2.0.1/
2. http://excellmedia.dl.sourceforge.net/project/subread/subread-2.0.1/
3. http://freefr.dl.sourceforge.net/project/subread/subread-2.0.1/
4. http://jaist.dl.sourceforge.net/project/subread/subread-2.0.1/
5. http://kent.dl.sourceforge.net/project/subread/subread-2.0.1/
6. http://nchc.dl.sourceforge.net/project/subread/subread-2.0.1/
7. http://netcologne.dl.sourceforge.net/project/subread/subread-2.0.1/
8. http://netix.dl.sourceforge.net/project/subread/subread-2.0.1/
9. http://superb-dca2.dl.sourceforge.net/project/subread/subread-2.0.1/
10. http://superb-sea2.dl.sourceforge.net/project/subread/subread-2.0.1/
11. http://ufpr.dl.sourceforge.net/project/subread/subread-2.0.1/
12. http://vorboss.dl.sourceforge.net/project/subread/subread-2.0.1/
13. https://downloads.sourceforge.net/project/subread/subread-2.0.1/
14. https://excellmedia.dl.sourceforge.net/project/subread/subread-2.0.1/
15. https://freefr.dl.sourceforge.net/project/subread/subread-2.0.1/
16. https://jaist.dl.sourceforge.net/project/subread/subread-2.0.1/
17. https://kent.dl.sourceforge.net/project/subread/subread-2.0.1/
18. https://nchc.dl.sourceforge.net/project/subread/subread-2.0.1/
19. https://netcologne.dl.sourceforge.net/project/subread/subread-2.0.1/
20. https://netix.dl.sourceforge.net/project/subread/subread-2.0.1/
21. https://superb-dca2.dl.sourceforge.net/project/subread/subread-2.0.1/
22. https://superb-sea2.dl.sourceforge.net/project/subread/subread-2.0.1/
23. https://ufpr.dl.sourceforge.net/project/subread/subread-2.0.1/
24. https://vorboss.dl.sourceforge.net/project/subread/subread-2.0.1/

biology/subread: Read alignment, quantification and mutation discovery

The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.

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Last updated:
2020-08-09 09:02:56