Kwalitee Issues


Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.


Add a META.json to the distribution. Your buildtool should be able to autogenerate it.


If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.


Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.


Name Abstract Version View
Bio::Roary Create a pan genome 3.007000 metacpan
Bio::Roary::AccessoryBinaryFasta Output a FASTA file which represents the binary presence and absence of genes in the accessory genome 3.007000 metacpan
Bio::Roary::AccessoryClustering Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters 3.007000 metacpan
Bio::Roary::AnalyseGroups Take in a groups file and the original FASTA files and create plots and stats 3.007000 metacpan
Bio::Roary::AnnotateGroups Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name 3.007000 metacpan
Bio::Roary::AssemblyStatistics Given a spreadsheet of gene presence and absence calculate some statistics 3.007000 metacpan
Bio::Roary::BedFromGFFRole A role to create a bed file from a gff 3.007000 metacpan
Bio::Roary::ChunkFastaFile Take in a FASTA file and chunk it up into smaller pieces. 3.007000 metacpan
Bio::Roary::ClustersRole A role to read a clusters file from CD hit 3.007000 metacpan
Bio::Roary::CombinedProteome Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's 3.007000 metacpan
Bio::Roary::CommandLine::AssemblyStatistics Given a spreadsheet of gene presence and absence calculate some statistics 3.007000 metacpan
Bio::Roary::CommandLine::Common Common command line settings 3.007000 metacpan
Bio::Roary::CommandLine::CreatePanGenome Take in FASTA files of proteins and cluster them 3.007000 metacpan
Bio::Roary::CommandLine::ExtractProteomeFromGff Take in GFF files and output the proteome 3.007000 metacpan
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides Take in a multifasta file of nucleotides, convert to proteins and align with PRANK 3.007000 metacpan
Bio::Roary::CommandLine::IterativeCdhit Iteratively run cdhit 3.007000 metacpan
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp Take in a FASTA file of proteins and blast against itself 3.007000 metacpan
Bio::Roary::CommandLine::QueryRoary Take in a groups file and the protein fasta files and output selected data 3.007000 metacpan
Bio::Roary::CommandLine::Roary Take in FASTA files of proteins and cluster them 3.007000 metacpan
Bio::Roary::CommandLine::RoaryCoreAlignment Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment. 3.007000 metacpan
Bio::Roary::CommandLine::RoaryPostAnalysis Perform the post analysis on the pan genome 3.007000 metacpan
Bio::Roary::CommandLine::RoaryReorderSpreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet 3.007000 metacpan
Bio::Roary::CommandLine::TransferAnnotationToGroups Take in a groups file and a set of GFF files and transfer the consensus annotation 3.007000 metacpan
Bio::Roary::ContigsToGeneIDsFromGFF Parse a GFF and efficiently and extract ordered gene ids on each contig 3.007000 metacpan
Bio::Roary::Exceptions Exceptions for input data 3.007000 metacpan
Bio::Roary::External::Blastp Wrapper around NCBIs blastp command 3.007000 metacpan
Bio::Roary::External::Cdhit Wrapper to run cd-hit 3.007000 metacpan
Bio::Roary::External::CheckTools Check external executables are available and are the correct version 3.007000 metacpan
Bio::Roary::External::Fasttree Wrapper to run Fasttree 3.007000 metacpan
Bio::Roary::External::GeneAlignmentFromNucleotides Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT 3.007000 metacpan
Bio::Roary::External::IterativeCdhit Iteratively run CDhit 3.007000 metacpan
Bio::Roary::External::Mafft Wrapper to run mafft 3.007000 metacpan
Bio::Roary::External::Makeblastdb Wrapper around NCBIs makeblastdb command 3.007000 metacpan
Bio::Roary::External::Mcl Wrapper around MCL which takes in blast results and outputs clustered results 3.007000 metacpan
Bio::Roary::External::PostAnalysis Perform the post analysis 3.007000 metacpan
Bio::Roary::External::Prank Wrapper to run prank 3.007000 metacpan
Bio::Roary::ExtractCoreGenesFromSpreadsheet Take in a spreadsheet produced by the pipeline and identify the core genes. 3.007000 metacpan
Bio::Roary::ExtractProteomeFromGFF Take in a GFF file and create protein sequences in FASTA format 3.007000 metacpan
Bio::Roary::ExtractProteomeFromGFFs Take in GFF files and create protein sequences in FASTA format 3.007000 metacpan
Bio::Roary::FilterFullClusters Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters 3.007000 metacpan
Bio::Roary::FilterUnknownsFromFasta Take in fasta files, remove sequences with too many unknowns and return a list of the new files 3.007000 metacpan
Bio::Roary::GeneNamesFromGFF Parse a GFF and efficiently extract ID -> Gene Name 3.007000 metacpan
Bio::Roary::GroupLabels Add labels to the groups 3.007000 metacpan
Bio::Roary::GroupStatistics Add labels to the groups 3.007000 metacpan
Bio::Roary::InflateClusters Take the clusters file from cd-hit and use it to inflate the output of MCL 3.007000 metacpan
Bio::Roary::IterativeCdhit Run CDhit iteratively with reducing thresholds, removing full clusters each time 3.007000 metacpan
Bio::Roary::JobRunner::Local Execute a set of commands locally 3.007000 metacpan
Bio::Roary::JobRunner::Parallel Use GNU Parallel 3.007000 metacpan
Bio::Roary::JobRunner::Role A role to add job runner functionality 3.007000 metacpan
Bio::Roary::LookupGeneFiles Take in an ordering of genes and a directory and return an ordered list of file locations 3.007000 metacpan
Bio::Roary::MergeMultifastaAlignments Merge multifasta alignment files with equal numbers of sequences. 3.007000 metacpan
Bio::Roary::OrderGenes Take in GFF files and create a matrix of what genes are beside what other genes 3.007000 metacpan
Bio::Roary::Output::BlastIdentityFrequency Take in blast results and find the percentage identity graph 3.007000 metacpan
Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL Create an embl file for the header with locations of where genes are in the multifasta alignment of core genes 3.007000 metacpan
Bio::Roary::Output::DifferenceBetweenSets Given two sets of isolates and a group file, output whats unique in each and whats in common 3.007000 metacpan
Bio::Roary::Output::EMBLHeaderCommon a role containing some common methods for embl header files 3.007000 metacpan
Bio::Roary::Output::EmblGroups Create a tab/embl file with the features for drawing pretty pictures 3.007000 metacpan
Bio::Roary::Output::GroupMultifasta Take in a group and create a multifasta file 3.007000 metacpan
Bio::Roary::Output::GroupsMultifastaNucleotide Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. 3.007000 metacpan
Bio::Roary::Output::GroupsMultifastaProtein Take a multifasta nucleotide file and output it as proteins. 3.007000 metacpan
Bio::Roary::Output::GroupsMultifastas Take in a list of groups and create multifastas files for each group 3.007000 metacpan
Bio::Roary::Output::GroupsMultifastasNucleotide Take in a set of GFF files and a groups file and output one multifasta file per group with nucleotide sequences. 3.007000 metacpan
Bio::Roary::Output::NumberOfGroups Create raw output files of group counts for turning into plots 3.007000 metacpan
Bio::Roary::Output::QueryGroups Output the groups of the union of a set of input isolates 3.007000 metacpan
Bio::Roary::ParallelAllAgainstAllBlast Run all against all blast in parallel 3.007000 metacpan
Bio::Roary::ParseGFFAnnotationRole A role for parsing a gff file efficiently 3.007000 metacpan
Bio::Roary::PostAnalysis Post analysis of pan genomes 3.007000 metacpan
Bio::Roary::PrepareInputFiles Take in a mixture of FASTA and GFF input files and output FASTA proteomes only 3.007000 metacpan
Bio::Roary::PresenceAbsenceMatrix Create a matrix with presence and absence 3.007000 metacpan
Bio::Roary::QC::Report generate a report based on kraken output 3.007000 metacpan
Bio::Roary::ReformatInputGFFs Take in gff files and add suffix where a gene id is seen twice 3.007000 metacpan
Bio::Roary::ReorderSpreadsheet Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns 3.007000 metacpan
Bio::Roary::SampleOrder Take in a tree file and return an ordering of the samples 3.007000 metacpan
Bio::Roary::SequenceLengths Take in a fasta file and create a hash with the length of each sequence 3.007000 metacpan
Bio::Roary::SortFasta sort a fasta file by name 3.007000 metacpan
Bio::Roary::SplitGroups split groups 3.007000 metacpan
Bio::Roary::SpreadsheetRole Read and write a spreadsheet 3.007000 metacpan

Other Files

MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan metacpan
dist.ini metacpan