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Paket: reapr (1.0.18+dfsg-5build1)

universal tool for genome assembly evaluation

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

Andra paket besläktade med reapr

  • beror
  • rekommenderar
  • föreslår
  • dep: bamtools
    toolkit for manipulating BAM (genome alignment) files
  • dep: libbamtools2.5.1 (>= 2.5.1+dfsg)
    dynamic library for manipulating BAM (genome alignment) files
  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    också ett virtuellt paket som tillhandahålls av libc6-udeb
    dep: libc6 (>= 2.4) [armhf]
  • dep: libfile-copy-link-perl
    Perl extension for replacing a link by a copy of the linked file
  • dep: libgcc-s1 (>= 3.0) [amd64]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libstdc++6 (>= 5.2) [armhf]
    GNU Standard C++ Library v3
    dep: libstdc++6 (>= 9) [amd64]
  • dep: libtabixpp0 (>= 1.0.0)
    C++ wrapper to tabix indexer
  • dep: r-base
    GNU R statistical computation and graphics system
  • dep: samtools (>= 1.3)
    processing sequence alignments in SAM, BAM and CRAM formats
  • dep: smalt
    Sequence Mapping and Alignment Tool
  • dep: snpomatic
    fast, stringent short-read mapping software
  • dep: tabix
    generic indexer for TAB-delimited genome position files

Hämta reapr

Hämtningar för alla tillgängliga arkitekturer
Arkitektur Paketstorlek Installerad storlek Filer
amd64 194,9 kbyte1073 kbyte [filförteckning]
armhf 164,6 kbyte643 kbyte [filförteckning]