Source: ncbi-vdb Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 12~), d-shlibs (>= 0.82), libbz2-dev, libxml2-dev, libhdf5-dev, libmagic-dev, libngs-sdk-dev, libngs-java, libmbedtls-dev, zlib1g-dev, default-jdk-headless Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-vdb Vcs-Git: https://salsa.debian.org/med-team/ncbi-vdb.git Homepage: https://github.com/ncbi/ncbi-vdb Package: libncbi-vdb2 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: libraries for using data in the INSDC Sequence Read Archives NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java. Package: libncbi-vdb-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends}, libncbi-vdb2 (= ${binary:Version}), libkdf5-dev (= ${binary:Version}), libncbi-wvdb-dev (= ${binary:Version}), libaec-dev, libbz2-dev, zlib1g-dev Description: libraries for using data in the INSDC Sequence Read Archives (devel) Much of the data submitted these days, for example in BAM, Illumina export.txt, and Complete Genomics formats, contain alignment information. With aligned data, NCBI uses Compression by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, for example as FastQ, requires fast access to the reference sequences that the original data was aligned to. NCBI recommends that SRA users dedicate local disk space to store references downloaded from the NCBI SRA site. As of Fall 2014, the complete collection of these reference sequences is 66 GB. While it isn't usually necessary to download the entirety of the reference sequences, this should give you an idea of the scale of the storage requirement. By default, the Toolkit will download missing reference sequences on demand and cache them in the user's home directory. The location of this cache is configurable, as is whether the download is automatic or manual. . This is the development package. Package: libkdf5-2 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends}, libmbedtls-dev Description: hdf5 access to data in the INSDC Sequence Read Archives NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . This library is part of the ncbi-vdb package and provides an interface to the Hierarchical Data Format 5 (HDF5). Package: libkdf5-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends}, libkdf5-2 (= ${binary:Version}) Description: hdf5 access to data in the INSDC Sequence Read Archives (devel) NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . This library is part of the ncbi-vdb package and provides an interface to the Hierarchical Data Format 5 (HDF5). . This is the development package. Package: libncbi-wvdb2 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: virtual layer update modul of ncbi-vdb library NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . This library is part of the ncbi-vdb package. Package: libncbi-wvdb-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends}, libncbi-wvdb2 (= ${binary:Version}) Description: virtual layer update modul of ncbi-vdb library (devel) NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . This library is part of the ncbi-vdb package. . This is the development package. Package: libvdb-sqlite2 Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: sqlite modul of ncbi-vdb library NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . This library is part of the ncbi-vdb package and provides a sqlite interface. Package: libvdb-sqlite-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends}, libvdb-sqlite2 (= ${binary:Version}) Description: sqlite modul of ncbi-vdb library (devel) NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb. . This library is part of the ncbi-vdb package and provides a sqlite interface. . This is the development package.