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Source: rapmap
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Michael R. Crusoe <michael.crusoe@gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
cmake,
zlib1g-dev,
libdivsufsort-dev,
libcereal-dev,
libjellyfish-2.0-dev,
libjemalloc-dev,
libsparsehash-dev,
libspdlog-dev,
libtclap-dev,
pkg-config,
python3-markdown,
python3
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/rapmap
Vcs-Git: https://salsa.debian.org/med-team/rapmap.git
Homepage: https://github.com/COMBINE-lab/RapMap
Package: rapmap
Architecture: amd64
Depends: ${shlibs:Depends},
${misc:Depends}
Description: rapid sensitive and accurate DNA read mapping via quasi-mapping
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
somewhat experimental. The develop branch will have the latest
improvements and additions, but is not guaranteed to be stable between
commits. Breaking changes to the master branch will be accompanied by a
tag to the version before the breaking change. Currently, RapMap is a
stand-alone quasi-mapper that can be used with other tools. It is also
being used as part of Sailfish and Salmon. Eventually, the hope is to
create and stabilize an API so that it can be used as a library from
other tools.
.
Quasi-mapping / (lightweight / pseudo)-alignment is the term that is
used here for the type of information required for certain tasks (e.g.
transcript quantification) that is less "heavyweight" than what is
provided by traditional alignment. For example, one may only need to
know the transcripts / contigs to which a read aligns and, perhaps, the
position within those transcripts rather than the optimal alignment and
base-for-base CIGAR string that aligns the read and substring of the
transcript. For details on RapMap (quasi-mapping in particular), please
check out the associated paper. Note: RapMap implements both quasi-
mapping and pseudo-alignment (originally introduced in Bray et al.
2016), these two are not the same thing. They are distinct concepts, and
RapMap simply happens to implement algorithms for computing both.
Package: rapmap-example-data
Architecture: all
Multi-Arch: foreign
Depends: ${misc:Depends}
Recommends: rapmap
Description: example data for rapmap - rapid sensitive and accurate DNA read mapping
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
somewhat experimental. The develop branch will have the latest
improvements and additions, but is not guaranteed to be stable between
commits. Breaking changes to the master branch will be accompanied by a
tag to the version before the breaking change. Currently, RapMap is a
stand-alone quasi-mapper that can be used with other tools. It is also
being used as part of Sailfish and Salmon. Eventually, the hope is to
create and stabilize an API so that it can be used as a library from
other tools.
.
This package contains example data to test this program.
Package: rapmap-dev
Architecture: all
Multi-Arch: foreign
Depends: ${misc:Depends}
Description: rapmap - rapid sensitive and accurate DNA read mapping (some headers)
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
somewhat experimental. The develop branch will have the latest
improvements and additions, but is not guaranteed to be stable between
commits. Breaking changes to the master branch will be accompanied by a
tag to the version before the breaking change. Currently, RapMap is a
stand-alone quasi-mapper that can be used with other tools. It is also
being used as part of Sailfish and Salmon. Eventually, the hope is to
create and stabilize an API so that it can be used as a library from
other tools.
.
This package contains some headers and C++ source files which are
included by package salmon and are provided here in an accessible
way to avoid code duplication. Usually there is no reason to install
this package except to build the salmon package.
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