Package: reapr (1.0.18+dfsg-6)

[ Source: reapr  ]

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.

Tags: Biology: Nucleic Acids, Field: Biology, field::biology:bioinformatics, implemented-in::c++, User Interface: Command Line, Role: role::program, works-with::biological-sequence

Other Packages Related to reapr

• dep: bamtools

  toolkit for manipulating BAM (genome alignment) files

• dep: libbamtools2.5.2 (>= 2.5.2+dfsg)

  dynamic library for manipulating BAM (genome alignment) files

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libfile-copy-link-perl

  Perl extension for replacing a link by a copy of the linked file

• dep: libgcc-s1 (>= 3.0) [not armel, armhf]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

• dep: libtabixpp0t64 (>= 1.0.0)

  C++ wrapper to tabix indexer

• dep: r-base

  GNU R statistical computation and graphics system

• dep: samtools

  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

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Architecture	Package Size	Installed Size	Files
amd64	202.3 kB	1,069.0 kB	[list of files]
arm64	176.0 kB	1,221.0 kB	[list of files]
armel	168.9 kB	847.0 kB	[list of files]
armhf	170.8 kB	643.0 kB	[list of files]
i386	208.9 kB	1,035.0 kB	[list of files]
mips64el	187.0 kB	1,642.0 kB	[list of files]
ppc64el	195.4 kB	1,669.0 kB	[list of files]
s390x	189.9 kB	1,001.0 kB	[list of files]