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Paketti: libseqlib2 (1.2.0+dfsg-8build1)

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

C++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C++ sequence analysis APIs. Minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment.

Muut pakettiin libseqlib2 liittyvät paketit

  • depends
  • recommends
  • suggests
  • dep: libc6 (>= 2.33)
    GNU C Library: Shared libraries
    myös näennäispaketti, jonka toteuttaa libc6-udeb
  • dep: libfml0 (>= 0.1+git20190320.b499514)
    library for assembling Illumina short reads in small regions
  • dep: libgcc-s1 (>= 3.0) [ei armhf]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libhts3 (>= 1.10)
    C library for high-throughput sequencing data formats
  • dep: libjsoncpp25 (>= 1.9.5)
    library for reading and writing JSON for C++
  • dep: libssw0 (>= 1.1)
    fast SIMD parallelized implementation of the Smith-Waterman algorithm
  • dep: libstdc++6 (>= 11)
    GNU Standard C++ Library v3
  • dep: zlib1g (>= 1:1.1.4)
    compression library - runtime

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amd64 170.6 kt552 kt [tiedostoluettelo]
arm64 158.2 kt443 kt [tiedostoluettelo]
armhf 147.7 kt318 kt [tiedostoluettelo]
ppc64el 194.4 kt596 kt [tiedostoluettelo]