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

  BAM (게놈 정렬) 파일을 조작하기 위한 툴킷

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

  dynamic library for manipulating BAM (genome alignment) files

• dep: libc6 (>= 2.34)

  GNU C 라이브러리: 공유 라이브러리
  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)

  GCC 기능 지원 라이브러리

• dep: libstdc++6 (>= 13.1)

  GNU 표준 C++ 라이브러리 v3

• dep: libtabixpp0t64 (>= 1.0.0)

  C++ wrapper to tabix indexer

• dep: r-base

  GNU R statistical computation and graphics system

• dep: samtools

  SAM, BAM, CRAM 형식에서 시퀀스 정렬 처리

• dep: smalt

  Sequence Mapping and Alignment Tool

• dep: snpomatic

  fast, stringent short-read mapping software

• dep: tabix

  TAB으로 구분된 게놈 위치 파일용 일반 인덱서

Download reapr

Download for all available architectures

Architecture	Package Size	Installed Size	Files
s390x	189.9 kB	1,001.0 kB	[list of files]