Package: roary (3.13.0+dfsg-1)

[ Source: 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.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::perl, interface::commandline, Role: Program, Scope: Utility, Purpose: use::analysing, use::comparing

Other Packages Related to roary

• dep: bedtools

  suite of utilities for comparing genomic features

• dep: bioperl (>= 1.7.4)

  Perl tools for computational molecular biology

• 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

  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

  module that allows you to declare real exception classes in Perl

• dep: libfile-find-rule-perl

  module to search for files based on rules

• 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 module for searching paths for executable programs

• 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

  modern Perl object system framework

• 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

  comma-separated values manipulator (using XS or 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

  build and execute command lines from standard input in parallel

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: prank

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

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: r-cran-ggplot2

  implementation of the Grammar of Graphics

Download roary

Download for all available architectures

Architecture	Package Size	Installed Size	Files
all	179.4 kB	670.0 kB	[list of files]