Balík: reapr (1.0.18+dfsg-6)

Odkazy pre reapr

Zdroje Debian:

Stiahnuť zdrojový balík reapr:

Správcovia:

Externé zdroje:

Domovská stránka [www.sanger.ac.uk]

Podobné balíky:

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.

Značky: Biológia: Nucleic Acids, Pole: Biológia, field::biology:bioinformatics, implemented-in::c++, User Interface: Príkazový riadok, Role: role::program, works-with::biological-sequence

Ostatné balíky súvisiace s balíkom reapr

závisí

odporúča

navrhuje

vylepšuje

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)

knižnica GNU C - zdieľané knižnice
tiež virtuálny balík poskytovaný balíkom 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)

podporná knižnica GCC
dep: libstdc++6 (>= 13.1)

štandardná knižnica C++ GNU 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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