[ 原始碼： roary ]
套件：roary（3.13.0+dfsg-1）
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.
其他與 roary 有關的套件
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- dep: bedtools
- suite of utilities for comparing genomic features
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- dep: bioperl (>= 1.7.4)
- Perl tools for computational molecular biology
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- dep: cd-hit
- suite of programs designed to quickly group sequences
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- dep: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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- dep: libarray-utils-perl
- collection of small utils for array manipulation
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- dep: libdigest-md5-file-perl
- Perl extension for getting MD5 sums for files and urls
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- dep: libenv-path-perl
- Perl module implementing advanced operations on path variables
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- dep: libexception-class-perl
- module that allows you to declare real exception classes in Perl
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- dep: libfile-find-rule-perl
- module to search for files based on rules
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- dep: libfile-grep-perl
- module for pattern matching in a series of files
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- dep: libfile-slurper-perl
- simple, sane and efficient module to slurp a file
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- dep: libfile-which-perl
- Perl module for searching paths for executable programs
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- dep: libfindbin-libs-perl
- Perl module to use a relative path for lib directories
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- dep: libgraph-perl
- Perl module for graph data structures and algorithms
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- dep: libgraph-readwrite-perl
- module for reading and writing directed graphs
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- dep: liblog-log4perl-perl
- Perl port of the widely popular log4j logging package
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- dep: libmoose-perl
- modern Perl object system framework
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- dep: libperlio-utf8-strict-perl
- fast and correct UTF-8 Perl IO module
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- dep: libtest-file-perl
- Perl module to test file attributes
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- dep: libtest-files-perl
- module to ease testing with files and directories
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- dep: libtest-most-perl
- Perl module with the most commonly needed test functions and features
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- dep: libtest-output-perl
- perl module to test stdout and stderr messages
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- dep: libtext-csv-perl
- comma-separated values manipulator (using XS or PurePerl)
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- dep: mafft
- Multiple alignment program for amino acid or nucleotide sequences
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- dep: mcl
- Markov Cluster algorithm
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- dep: ncbi-blast+
- next generation suite of BLAST sequence search tools
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- dep: parallel
- build and execute command lines from standard input in parallel
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- dep: perl
- Larry Wall's Practical Extraction and Report Language
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- dep: prank
- Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
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- dep: r-base-core
- GNU R core of statistical computation and graphics system
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- dep: r-cran-ggplot2
- implementation of the Grammar of Graphics