Kwalitee Issues

has_changelog

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

meta_yml_declares_perl_version

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.

Modules

Name Abstract Version View
Bio::Roary Create a pan genome v3.12.0 metacpan
Bio::Roary::AccessoryBinaryFasta Output a FASTA file which represents the binary presence and absence of genes in the accessory genome v3.12.0 metacpan
Bio::Roary::AccessoryClustering Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters v3.12.0 metacpan
Bio::Roary::AnalyseGroups Take in a groups file and the original FASTA files and create plots and stats v3.12.0 metacpan
Bio::Roary::AnnotateGroups Take in a group file and associated GFF files for the isolates and update the group name to the gene name v3.12.0 metacpan
Bio::Roary::AssemblyStatistics Given a spreadsheet of gene presence and absence calculate some statistics v3.12.0 metacpan
Bio::Roary::BedFromGFFRole A role to create a bed file from a gff v3.12.0 metacpan
Bio::Roary::ChunkFastaFile Take in a FASTA file and chunk it up into smaller pieces. v3.12.0 metacpan
Bio::Roary::ClustersRole A role to read a clusters file from CD hit v3.12.0 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 v3.12.0 metacpan
Bio::Roary::CommandLine::AssemblyStatistics Given a spreadsheet of gene presence and absence calculate some statistics v3.12.0 metacpan
Bio::Roary::CommandLine::Common Common command line settings v3.12.0 metacpan
Bio::Roary::CommandLine::CreatePanGenome Take in FASTA files of proteins and cluster them v3.12.0 metacpan
Bio::Roary::CommandLine::ExtractProteomeFromGff Take in GFF files and output the proteome v3.12.0 metacpan
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides Take in a multifasta file of nucleotides, convert to proteins and align with PRANK v3.12.0 metacpan
Bio::Roary::CommandLine::IterativeCdhit Iteratively run cdhit v3.12.0 metacpan
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp Take in a FASTA file of proteins and blast against itself v3.12.0 metacpan
Bio::Roary::CommandLine::QueryRoary Take in a groups file and the protein fasta files and output selected data v3.12.0 metacpan
Bio::Roary::CommandLine::Roary Take in FASTA files of proteins and cluster them v3.12.0 metacpan
Bio::Roary::CommandLine::RoaryCoreAlignment Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment. v3.12.0 metacpan
Bio::Roary::CommandLine::RoaryPostAnalysis Perform the post analysis on the pan genome v3.12.0 metacpan
Bio::Roary::CommandLine::RoaryReorderSpreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet v3.12.0 metacpan
Bio::Roary::CommandLine::TransferAnnotationToGroups Take in a groups file and a set of GFF files and transfer the consensus annotation v3.12.0 metacpan
Bio::Roary::CommandLine::UniqueGenesPerSample Take in the clustered file and produce a sorted file with the frequency of each samples unique genes v3.12.0 metacpan
Bio::Roary::ContigsToGeneIDsFromGFF Parse a GFF and efficiently and extract ordered gene ids on each contig v3.12.0 metacpan
Bio::Roary::Exceptions Exceptions for input data v3.12.0 metacpan
Bio::Roary::External::Blastp Wrapper around NCBIs blastp command v3.12.0 metacpan
Bio::Roary::External::Cdhit Wrapper to run cd-hit v3.12.0 metacpan
Bio::Roary::External::CheckTools Check external executables are available and are the correct version v3.12.0 metacpan
Bio::Roary::External::Fasttree Wrapper to run Fasttree v3.12.0 metacpan
Bio::Roary::External::GeneAlignmentFromNucleotides Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT v3.12.0 metacpan
Bio::Roary::External::IterativeCdhit Iteratively run CDhit v3.12.0 metacpan
Bio::Roary::External::Mafft Wrapper to run mafft v3.12.0 metacpan
Bio::Roary::External::Makeblastdb Wrapper around NCBIs makeblastdb command v3.12.0 metacpan
Bio::Roary::External::Mcl Wrapper around MCL which takes in blast results and outputs clustered results v3.12.0 metacpan
Bio::Roary::External::PostAnalysis Perform the post analysis v3.12.0 metacpan
Bio::Roary::External::Prank Wrapper to run prank v3.12.0 metacpan
Bio::Roary::ExtractCoreGenesFromSpreadsheet Take in a spreadsheet produced by the pipeline and identify the core genes. v3.12.0 metacpan
Bio::Roary::ExtractProteomeFromGFF Take in a GFF file and create protein sequences in FASTA format v3.12.0 metacpan
Bio::Roary::ExtractProteomeFromGFFs Take in GFF files and create protein sequences in FASTA format v3.12.0 metacpan
Bio::Roary::FilterFullClusters Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters v3.12.0 metacpan
Bio::Roary::FilterUnknownsFromFasta Take in fasta files, remove sequences with too many unknowns and return a list of the new files v3.12.0 metacpan
Bio::Roary::GeneNamesFromGFF Parse a GFF and efficiently extract ID -> Gene Name v3.12.0 metacpan
Bio::Roary::GroupLabels Add labels to the groups v3.12.0 metacpan
Bio::Roary::GroupStatistics Add labels to the groups v3.12.0 metacpan
Bio::Roary::InflateClusters Take the clusters file from cd-hit and use it to inflate the output of MCL v3.12.0 metacpan
Bio::Roary::IterativeCdhit Run CDhit iteratively with reducing thresholds, removing full clusters each time v3.12.0 metacpan
Bio::Roary::JobRunner::Local Execute a set of commands locally v3.12.0 metacpan
Bio::Roary::JobRunner::Parallel Use GNU Parallel v3.12.0 metacpan
Bio::Roary::JobRunner::Role A role to add job runner functionality v3.12.0 metacpan
Bio::Roary::LookupGeneFiles Take in an ordering of genes and a directory and return an ordered list of file locations v3.12.0 metacpan
Bio::Roary::MergeMultifastaAlignments Merge multifasta alignment files with equal numbers of sequences. v3.12.0 metacpan
Bio::Roary::OrderGenes Take in GFF files and create a matrix of what genes are beside what other genes v3.12.0 metacpan
Bio::Roary::Output::BlastIdentityFrequency Take in blast results and find the percentage identity graph v3.12.0 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 v3.12.0 metacpan
Bio::Roary::Output::DifferenceBetweenSets Given two sets of isolates and a group file, output whats unique in each and whats in common v3.12.0 metacpan
Bio::Roary::Output::EMBLHeaderCommon a role containing some common methods for embl header files v3.12.0 metacpan
Bio::Roary::Output::EmblGroups Create a tab/embl file with the features for drawing pretty pictures v3.12.0 metacpan
Bio::Roary::Output::GroupMultifasta Take in a group and create a multifasta file v3.12.0 metacpan
Bio::Roary::Output::GroupsMultifastaNucleotide Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. v3.12.0 metacpan
Bio::Roary::Output::GroupsMultifastaProtein Take a multifasta nucleotide file and output it as proteins. v3.12.0 metacpan
Bio::Roary::Output::GroupsMultifastas Take in a list of groups and create multifastas files for each group v3.12.0 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. v3.12.0 metacpan
Bio::Roary::Output::NumberOfGroups Create raw output files of group counts for turning into plots v3.12.0 metacpan
Bio::Roary::Output::QueryGroups Output the groups of the union of a set of input isolates v3.12.0 metacpan
Bio::Roary::ParallelAllAgainstAllBlast Run all against all blast in parallel v3.12.0 metacpan
Bio::Roary::ParseGFFAnnotationRole A role for parsing a gff file efficiently v3.12.0 metacpan
Bio::Roary::PostAnalysis Post analysis of pan genomes v3.12.0 metacpan
Bio::Roary::PrepareInputFiles Take in a mixture of FASTA and GFF input files and output FASTA proteomes only v3.12.0 metacpan
Bio::Roary::PresenceAbsenceMatrix Create a matrix with presence and absence v3.12.0 metacpan
Bio::Roary::QC::Report generate a report based on kraken output v3.12.0 metacpan
Bio::Roary::ReformatInputGFFs Take in gff files and add suffix where a gene id is seen twice v3.12.0 metacpan
Bio::Roary::ReorderSpreadsheet Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns v3.12.0 metacpan
Bio::Roary::SampleOrder Take in a tree file and return an ordering of the samples v3.12.0 metacpan
Bio::Roary::SequenceLengths Take in a fasta file and create a hash with the length of each sequence v3.12.0 metacpan
Bio::Roary::SortFasta sort a fasta file by name v3.12.0 metacpan
Bio::Roary::SplitGroups split groups v3.12.0 metacpan
Bio::Roary::SpreadsheetRole Read and write a spreadsheet v3.12.0 metacpan
Bio::Roary::UniqueGenesPerSample Take in the clustered file and produce a sorted file with the frequency of each samples unique genes v3.12.0 metacpan

Other Files

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