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Source: pbsuite
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pbsuite
Vcs-Git: https://salsa.debian.org/med-team/pbsuite.git
Homepage: http://sourceforge.net/projects/pb-jelly
Rules-Requires-Root: no
Package: pbsuite
Architecture: all
Section: metapackages
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: python3-pbsuite-utils
Architecture: all
Section: python
Depends: ${misc:Depends},
${python3:Depends},
python3-pysam
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 3 utilities for the suite.
Package: pbjelly
Architecture: all
Depends: ${misc:Depends},
${python3:Depends},
python3-pbsuite-utils (= ${source:Version}),
python3-networkx,
blasr
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},
${python3:Depends},
python3-pbsuite-utils (= ${source:Version}),
python3-pbbanana (= ${source:Version}),
python3-pysam,
python3-networkx,
python3-h5py,
python3-numpy,
python3-intervaltree-bio,
blasr,
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: python3-pbbanana
Architecture: all
Section: python
Depends: ${misc:Depends},
${python3:Depends},
python3-pbsuite-utils (= ${source:Version}),
python3-networkx,
pbjelly (= ${source:Version}),
blasr
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
|
