roary
high speed stand alone pan genome pipeline
Command lineScience
Not tested on a device yet. What that means
Commands in the package
roarycreate_pan_genomecreate_pan_genome_plotsextract_proteome_from_gffiterative_cdhitpan_genome_assembly_statisticspan_genome_core_alignmentpan_genome_post_analysispan_genome_reorder_spreadsheetparallel_all_against_all_blastpprotein_alignment_from_nucleotidesquery_pan_genomeroary-create_pan_genome_plotsroary-pan_genome_reorder_spreadsheetroary-query_pan_genomeroary-unique_genes_per_sampletransfer_annotation_to_groups
About roary
From Debian's package description
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.
From Debian's description of the roary package, under that package's license.
Dependencies
Depends on
perlbioperllibarray-utils-perllibdigest-md5-file-perllibenv-path-perllibexception-class-perllibfile-find-rule-perllibfile-grep-perllibfile-slurper-perllibfile-which-perllibfindbin-libs-perllibgraph-perllibgraph-readwrite-perlliblog-log4perl-perllibmoose-perllibperlio-utf8-strict-perllibtest-most-perllibtest-file-perllibtest-files-perllibtest-output-perllibtext-csv-perlbedtoolscd-hitncbi-blast+mclparallelprankr-base-corer-cran-ggplot2mafftfasttree
Related apps
- gdal-binGeospatial Data Abstraction Library - Utility programsCommand line
- plinkwhole-genome association analysis toolsetCommand line
- ncbi-blast+next generation suite of BLAST sequence search toolsCommand line
- gbrowseGMOD Generic Genome BrowserCommand line
- dolfin-binExecutable scripts for DOLFINCommand line
GwyddionSPM data visualization and analysis
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the roary package, under that package's license.
- Description: Debian's description of the roary package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.