Пакет: reapr (1.0.18+dfsg-6)

Връзки за reapr

Ресурси за Debian:

Изтегляне на пакет-източник reapr.

Отговорници:

Външни препратки:

Начална страница [www.sanger.ac.uk]

Подобни пакети:

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.

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

Други пакети, свързани с reapr

зависимости

препоръчани

предложени

enhances

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
също и виртуален пакет, предлаган от 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) [не 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

Изтегляне на reapr

Изтегляне за всички налични архитектури
Архитектура	Големина на пакета	Големина след инсталиране	Файлове
amd64	202,3 кБ	1 069,0 кБ	[списък на файловете]
arm64	176,0 кБ	1 221,0 кБ	[списък на файловете]
armel	168,9 кБ	847,0 кБ	[списък на файловете]
armhf	170,8 кБ	643,0 кБ	[списък на файловете]
i386	208,9 кБ	1 035,0 кБ	[списък на файловете]
mips64el	187,0 кБ	1 642,0 кБ	[списък на файловете]
ppc64el	195,4 кБ	1 669,0 кБ	[списък на файловете]
s390x	189,9 кБ	1 001,0 кБ	[списък на файловете]