Bio-Roary 3.13.0 Latest
Kwalitee Issues
No Core Issues.
- 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 | v3.13.0 | metacpan |
Bio::Roary::AccessoryBinaryFasta | Output a FASTA file which represents the binary presence and absence of genes in the accessory genome | v3.13.0 | metacpan |
Bio::Roary::AccessoryClustering | Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters | v3.13.0 | metacpan |
Bio::Roary::AnalyseGroups | Take in a groups file and the original FASTA files and create plots and stats | v3.13.0 | 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 | v3.13.0 | metacpan |
Bio::Roary::AssemblyStatistics | Given a spreadsheet of gene presence and absence calculate some statistics | v3.13.0 | metacpan |
Bio::Roary::BedFromGFFRole | A role to create a bed file from a gff | v3.13.0 | metacpan |
Bio::Roary::ChunkFastaFile | Take in a FASTA file and chunk it up into smaller pieces. | v3.13.0 | metacpan |
Bio::Roary::ClustersRole | A role to read a clusters file from CD hit | v3.13.0 | 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 | v3.13.0 | metacpan |
Bio::Roary::CommandLine::AssemblyStatistics | Given a spreadsheet of gene presence and absence calculate some statistics | v3.13.0 | metacpan |
Bio::Roary::CommandLine::Common | Common command line settings | v3.13.0 | metacpan |
Bio::Roary::CommandLine::CreatePanGenome | Take in FASTA files of proteins and cluster them | v3.13.0 | metacpan |
Bio::Roary::CommandLine::ExtractProteomeFromGff | Take in GFF files and output the proteome | v3.13.0 | metacpan |
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides | Take in a multifasta file of nucleotides, convert to proteins and align with PRANK | v3.13.0 | metacpan |
Bio::Roary::CommandLine::IterativeCdhit | Iteratively run cdhit | v3.13.0 | metacpan |
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp | Take in a FASTA file of proteins and blast against itself | v3.13.0 | metacpan |
Bio::Roary::CommandLine::QueryRoary | Take in a groups file and the protein fasta files and output selected data | v3.13.0 | metacpan |
Bio::Roary::CommandLine::Roary | Take in FASTA files of proteins and cluster them | v3.13.0 | metacpan |
Bio::Roary::CommandLine::RoaryCoreAlignment | Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment. | v3.13.0 | metacpan |
Bio::Roary::CommandLine::RoaryPostAnalysis | Perform the post analysis on the pan genome | v3.13.0 | metacpan |
Bio::Roary::CommandLine::RoaryReorderSpreadsheet | Take in a tree and a spreadsheet and output a reordered spreadsheet | v3.13.0 | metacpan |
Bio::Roary::CommandLine::TransferAnnotationToGroups | Take in a groups file and a set of GFF files and transfer the consensus annotation | v3.13.0 | metacpan |
Bio::Roary::CommandLine::UniqueGenesPerSample | Take in the clustered file and produce a sorted file with the frequency of each samples unique genes | v3.13.0 | metacpan |
Bio::Roary::ContigsToGeneIDsFromGFF | Parse a GFF and efficiently and extract ordered gene ids on each contig | v3.13.0 | metacpan |
Bio::Roary::Exceptions | Exceptions for input data | v3.13.0 | metacpan |
Bio::Roary::External::Blastp | Wrapper around NCBIs blastp command | v3.13.0 | metacpan |
Bio::Roary::External::Cdhit | Wrapper to run cd-hit | v3.13.0 | metacpan |
Bio::Roary::External::CheckTools | Check external executables are available and are the correct version | v3.13.0 | metacpan |
Bio::Roary::External::Fasttree | Wrapper to run Fasttree | v3.13.0 | metacpan |
Bio::Roary::External::GeneAlignmentFromNucleotides | Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT | v3.13.0 | metacpan |
Bio::Roary::External::IterativeCdhit | Iteratively run CDhit | v3.13.0 | metacpan |
Bio::Roary::External::Mafft | Wrapper to run mafft | v3.13.0 | metacpan |
Bio::Roary::External::Makeblastdb | Wrapper around NCBIs makeblastdb command | v3.13.0 | metacpan |
Bio::Roary::External::Mcl | Wrapper around MCL which takes in blast results and outputs clustered results | v3.13.0 | metacpan |
Bio::Roary::External::PostAnalysis | Perform the post analysis | v3.13.0 | metacpan |
Bio::Roary::External::Prank | Wrapper to run prank | v3.13.0 | metacpan |
Bio::Roary::ExtractCoreGenesFromSpreadsheet | Take in a spreadsheet produced by the pipeline and identify the core genes. | v3.13.0 | metacpan |
Bio::Roary::ExtractProteomeFromGFF | Take in a GFF file and create protein sequences in FASTA format | v3.13.0 | metacpan |
Bio::Roary::ExtractProteomeFromGFFs | Take in GFF files and create protein sequences in FASTA format | v3.13.0 | metacpan |
Bio::Roary::FilterFullClusters | Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters | v3.13.0 | metacpan |
Bio::Roary::FilterUnknownsFromFasta | Take in fasta files, remove sequences with too many unknowns and return a list of the new files | v3.13.0 | metacpan |
Bio::Roary::GeneNamesFromGFF | Parse a GFF and efficiently extract ID -> Gene Name | v3.13.0 | metacpan |
Bio::Roary::GroupLabels | Add labels to the groups | v3.13.0 | metacpan |
Bio::Roary::GroupStatistics | Add labels to the groups | v3.13.0 | metacpan |
Bio::Roary::InflateClusters | Take the clusters file from cd-hit and use it to inflate the output of MCL | v3.13.0 | metacpan |
Bio::Roary::IterativeCdhit | Run CDhit iteratively with reducing thresholds, removing full clusters each time | v3.13.0 | metacpan |
Bio::Roary::JobRunner::Local | Execute a set of commands locally | v3.13.0 | metacpan |
Bio::Roary::JobRunner::Parallel | Use GNU Parallel | v3.13.0 | metacpan |
Bio::Roary::JobRunner::Role | A role to add job runner functionality | v3.13.0 | metacpan |
Bio::Roary::LookupGeneFiles | Take in an ordering of genes and a directory and return an ordered list of file locations | v3.13.0 | metacpan |
Bio::Roary::MergeMultifastaAlignments | Merge multifasta alignment files with equal numbers of sequences. | v3.13.0 | metacpan |
Bio::Roary::OrderGenes | Take in GFF files and create a matrix of what genes are beside what other genes | v3.13.0 | metacpan |
Bio::Roary::Output::BlastIdentityFrequency | Take in blast results and find the percentage identity graph | v3.13.0 | 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 | v3.13.0 | metacpan |
Bio::Roary::Output::DifferenceBetweenSets | Given two sets of isolates and a group file, output whats unique in each and whats in common | v3.13.0 | metacpan |
Bio::Roary::Output::EMBLHeaderCommon | a role containing some common methods for embl header files | v3.13.0 | metacpan |
Bio::Roary::Output::EmblGroups | Create a tab/embl file with the features for drawing pretty pictures | v3.13.0 | metacpan |
Bio::Roary::Output::GroupMultifasta | Take in a group and create a multifasta file | v3.13.0 | metacpan |
Bio::Roary::Output::GroupsMultifastaNucleotide | Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. | v3.13.0 | metacpan |
Bio::Roary::Output::GroupsMultifastaProtein | Take a multifasta nucleotide file and output it as proteins. | v3.13.0 | metacpan |
Bio::Roary::Output::GroupsMultifastas | Take in a list of groups and create multifastas files for each group | v3.13.0 | 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. | v3.13.0 | metacpan |
Bio::Roary::Output::NumberOfGroups | Create raw output files of group counts for turning into plots | v3.13.0 | metacpan |
Bio::Roary::Output::QueryGroups | Output the groups of the union of a set of input isolates | v3.13.0 | metacpan |
Bio::Roary::ParallelAllAgainstAllBlast | Run all against all blast in parallel | v3.13.0 | metacpan |
Bio::Roary::ParseGFFAnnotationRole | A role for parsing a gff file efficiently | v3.13.0 | metacpan |
Bio::Roary::PostAnalysis | Post analysis of pan genomes | v3.13.0 | metacpan |
Bio::Roary::PrepareInputFiles | Take in a mixture of FASTA and GFF input files and output FASTA proteomes only | v3.13.0 | metacpan |
Bio::Roary::PresenceAbsenceMatrix | Create a matrix with presence and absence | v3.13.0 | metacpan |
Bio::Roary::QC::Report | generate a report based on kraken output | v3.13.0 | metacpan |
Bio::Roary::ReformatInputGFFs | Take in gff files and add suffix where a gene id is seen twice | v3.13.0 | metacpan |
Bio::Roary::ReorderSpreadsheet | Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns | v3.13.0 | metacpan |
Bio::Roary::SampleOrder | Take in a tree file and return an ordering of the samples | v3.13.0 | metacpan |
Bio::Roary::SequenceLengths | Take in a fasta file and create a hash with the length of each sequence | v3.13.0 | metacpan |
Bio::Roary::SortFasta | sort a fasta file by name | v3.13.0 | metacpan |
Bio::Roary::SplitGroups | split groups | v3.13.0 | metacpan |
Bio::Roary::SpreadsheetRole | Read and write a spreadsheet | v3.13.0 | metacpan |
Bio::Roary::UniqueGenesPerSample | Take in the clustered file and produce a sorted file with the frequency of each samples unique genes | v3.13.0 | metacpan |