eLxr packages [ bianca ]
[ ソース: shasta ]
パッケージ: python3-shasta (0.12.0-1 など)
nanopore whole genome assembly (dynamic library)
De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.
Computational methods used by the Shasta assembler include:
* Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
* Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).
Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers.
This package contains the dynamic library that can be interfaced and imported within Python.
その他の python3-shasta 関連パッケージ
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- dep: libblas3
- Basic Linear Algebra Reference implementations, shared library
- または libblas.so.3
- 以下のパッケージによって提供される仮想パッケージです: libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial
-
- dep: libboost-program-options1.83.0 (>= 1.83.0)
- program options library for C++
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- dep: libboost-serialization1.83.0 (>= 1.83.0)
- serialization library for C++
-
- dep: libc6 (>= 2.38)
- GNU C Library: Shared libraries
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
-
- dep: libgcc-s1 (>= 3.4)
- GCC support library
-
- dep: liblapack3
- Library of linear algebra routines 3 - shared version
- または liblapack.so.3
- 以下のパッケージによって提供される仮想パッケージです: liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial
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- dep: libpng16-16t64 (>= 1.6.2)
- PNG library - runtime (version 1.6)
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- dep: libpython3.13 (>= 3.13.0~rc3)
- Shared Python runtime library (version 3.13)
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- dep: libspoa7.0.0 (>= 4.0.5)
- SIMD partial order alignment library
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- dep: libstdc++6 (>= 14)
- GNU Standard C++ Library v3
-
- dep: ncbi-blast+
- next generation suite of BLAST sequence search tools
-
- dep: python3 (<< 3.14)
- interactive high-level object-oriented language (default python3 version)
- dep: python3 (>= 3.13~)