Paket: roary (3.12.0+dfsg-2)

[ Quellcode: 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.

Markierungen: Feld: Biologie, Bioinformatik, Implementiert in: implemented-in::perl, interface::commandline, Rolle: Programm, Zweck: Hilfswerkzeug, Zweck: use::analysing, use::comparing

Andere Pakete mit Bezug zu roary

• dep: bedtools

  Hilfswerkzeugsammlung zum Vergleich genomischer Merkmale

• dep: bioperl

  Perl-Werkzeuge für bioinformatische Anwendungen

• dep: cd-hit

  Programme zur schnellen Gruppierung von Sequenzen

• 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

  Perl extension for getting MD5 sums for files and urls

• dep: libenv-path-perl

  Perl module implementing advanced operations on path variables

• dep: libexception-class-perl

  Modul, das echte Perl-Klassen zur Behandlung von Ausnahmen deklarieren kann

• dep: libfile-find-rule-perl

  Modul zur regelbasierten Suche nach Dateien

• dep: libfile-grep-perl

  module for pattern matching in a series of files

• dep: libfile-slurper-perl

  simple, sane and efficient module to slurp a file

• dep: libfile-which-perl

  Perl-Modul zum Durchsuchen des Pfads nach ausführbaren Programmen

• 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-Portierung des sehr populären Protokollierungspakets log4j

• dep: libmoose-perl

  Modernes Rahmenwerk für das Perl-Objektsystem

• 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

  Manipulator für komma-getrennte Werte (mittels XS oder reinem Perl)

• dep: mafft

  Programm für multiples Alignment von Aminosäure- oder Nukleotidsequenzen

• dep: mcl

  Markov-Cluster-Algorithmus

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: parallel

  build and execute command lines from standard input in parallel

• dep: perl

  Larry Wall's Practical Extraction und Report Language

• dep: prank

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

• dep: r-base-core

  GNU R - System für statistische Berechnungen und Grafik - Kern

• dep: r-cran-ggplot2

  Implementierung der »Grammar of Graphics«

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