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Source: pbsuite
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
Afif Elghraoui <afif@debian.org>
Build-Depends:
debhelper (>= 9),
dh-python,
python-all,
Standards-Version: 3.9.8
Homepage: http://sourceforge.net/projects/pb-jelly
Vcs-Git: https://anonscm.debian.org/git/debian-med/pbsuite.git
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbsuite.git
Package: pbsuite
Section: metapackages
Architecture: all
Depends:
${misc:Depends},
pbjelly,
pbhoney,
Description: software for Pacific Biosciences sequencing data
The PBSuite contains two projects created for analysis of
Pacific Biosciences long-read sequencing data.
* PBJelly - genome upgrading tool
* PBHoney - structural variation discovery
Package: python-pbsuite-utils
Section: python
Architecture: all
Depends:
${misc:Depends},
${python:Depends},
python-pysam (>= 0.8.0),
Description: software for Pacific Biosciences sequencing data -- Python utilities
The PBSuite currently contains two projects created and maintained
by Adam English for analysis of Pacific Biosciences long-read
sequencing data.
* PBJelly - genome upgrading tool
* PBHoney - structural variation discovery
.
This package contains Python 2 utilities for the suite.
Package: pbjelly
Architecture: all
Depends:
${misc:Depends},
${python:Depends},
python-pbsuite-utils (= ${source:Version}),
python-networkx,
blasr (>= 5.3),
Description: genome assembly upgrading tool
PBJelly is a highly automated pipeline that aligns long sequencing
reads (such as PacBio RS reads or long 454 reads in fasta format)
to high-confidence draft assembles. PBJelly fills or reduces as
many captured gaps as possible to produce upgraded draft genomes.
.
PBJelly is part of the PBSuite.
Package: pbhoney
Architecture: all
Depends:
${misc:Depends},
${python:Depends},
python-pbsuite-utils (= ${source:Version}),
python-pbbanana (= ${source:Version}),
python-pysam (>= 0.8.0),
python-networkx,
python-h5py (>= 2.0.1),
python-numpy,
python-intervaltree-bio,
blasr (>= 5.3),
samtools,
Recommends:
pbdagcon,
Description: genomic structural variation discovery
PBHoney is an implementation of two variant-identification
approaches designed to exploit the high mappability of long reads
(i.e., greater than 10,000 bp). PBHoney considers both intra-read
discordance and soft-clipped tails of long reads to identify
structural variants.
.
PBHoney is part of the PBSuite.
Package: python-pbbanana
Section: python
Depends:
${misc:Depends},
${python:Depends},
python-pbsuite-utils (= ${source:Version}),
python-networkx,
pbjelly (= ${source:Version}),
blasr,
Architecture: all
Description: additional utilities for the pbsuite
PBBanana contains some assembly and consensus utilities
for the PBSuite.
* OLCAssembly - A shortcut to calling pacbio's Allora Assembler
* Polish - A quick consensus caller
* PBJNovo - DeNovo Assembler of PacBio only reads
.
This package is intended for use internally by the PBSuite
|
