Balík: roary (3.13.0+dfsg-1)

[ Zdroj: roary  ]

high speed stand alone pan genome pipeline

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.

Značky: Pole: Biológia, Bioinformatika, Implementované v: implemented-in::perl, interface::commandline, Role: Program, Scope: Utility, Purpose: use::analysing, use::comparing

Ostatné balíky súvisiace s balíkom roary

• dep: bedtools

  suite of utilities for comparing genomic features

• dep: bioperl (>= 1.7.4)

  nástroje jazyka Perl na výpočtovú molekulárnu biológiu

• dep: cd-hit

  suite of programs designed to quickly group sequences

• dep: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: libarray-utils-perl

  collection of small utils for array manipulation

• dep: libdigest-md5-file-perl

  rozšírenie jazyka Perl na výpočet súčtov MD5 súborov a url

• dep: libenv-path-perl

  Perl module implementing advanced operations on path variables

• dep: libexception-class-perl

  modul jazyka Perl, ktorý vám umožňuje deklarovať skutočné triedy výnimiek

• dep: libfile-find-rule-perl

  modul na hľadanie súborov na základe pravidiel

• dep: libfile-grep-perl

  module for pattern matching in a series of files

• dep: libfile-slurper-perl

  jednoduchý, rozumný a efektívny modul na sťahovanie súborov

• dep: libfile-which-perl

  modul Perlu na nájdenie ciest k spustiteľným programom

• dep: libfindbin-libs-perl

  Perl module to use a relative path for lib directories

• dep: libgraph-perl

  Perl module for graph data structures and algorithms

• dep: libgraph-readwrite-perl

  module for reading and writing directed graphs

• dep: liblog-log4perl-perl

  Perl port of the widely popular log4j logging package

• dep: libmoose-perl

  moderná platforma objektového systému jazyka Perl

• dep: libperlio-utf8-strict-perl

  fast and correct UTF-8 Perl IO module

• dep: libtest-file-perl

  Perl module to test file attributes

• dep: libtest-files-perl

  module to ease testing with files and directories

• dep: libtest-most-perl

  Perl module with the most commonly needed test functions and features

• dep: libtest-output-perl

  perl module to test stdout and stderr messages

• dep: libtext-csv-perl

  manipulátor súborov CSV (pomocou XS alebo PurePerl)

• dep: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• dep: mcl

  Markov Cluster algorithm

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: parallel

  príprava a paralelné spúšťanie príkazových riadkov zo štandardného vstupu

• dep: perl

  Practical Extraction and Report Language od Larryho Walla

• dep: prank

  Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

• dep: r-base-core

  jadro GNU R na štatistické výpočty a grafický systém

• dep: r-cran-ggplot2

  implementácia Gramatiky grafiky

Stiahnuť roary

Stiahnuť pre všetky dostupné architektúry

Architektúra	Veľkosť balíka	Nainštalovaná veľkosť	Súbory
all	179.4 kB	670.0 kB	[zoznam súborov]