Source: rapmap Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Section: science Priority: optional Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3 Standards-Version: 4.6.1 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 Rules-Requires-Root: no Package: rapmap Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Built-Using: ${simde:Built-Using} 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.