套件：reapr（1.0.18+dfsg-7）

[ 原始碼： 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.

標籤: 生物學: 核酸, 領域: 生物學, field::biology:bioinformatics, implemented-in::c++, 使用者介面: 命令行, 角色: role::program, works-with::biological-sequence

其他與 reapr 有關的套件

• 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 (>= 2.38)

  GNU C 函式庫：共用函式庫
  同時作為一個虛擬套件由這些套件填實： 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) [除 armel, armhf, riscv64]

  GCC 支援函式庫

  dep: libgcc-s1 (>= 3.4) [riscv64]

  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

下載 reapr

下載可用於所有硬體架構的

硬體架構	套件大小	安裝後大小	檔案
amd64	209。9 kB	1，073。0 kB	[檔案列表]
arm64	178。9 kB	1，221。0 kB	[檔案列表]
armel	171。8 kB	1，207。0 kB	[檔案列表]
armhf	174。4 kB	1，143。0 kB	[檔案列表]
i386	212。8 kB	1，035。0 kB	[檔案列表]
mips64el	193。0 kB	1，640。0 kB	[檔案列表]
ppc64el	198。2 kB	1，669。0 kB	[檔案列表]
riscv64	192。4 kB	753。0 kB	[檔案列表]
s390x	192。7 kB	993。0 kB	[檔案列表]