Bio-Roary 3.7.0
- Released by
- AJPAGE
- Version
- Release Date
- 2016-09-24
- Kwalitee
- 150
- Core Kwalitee
- 96.88
- LINKS
Bio-Roary 3.7.0 Deleted
Kwalitee Issues
This is not the latest release. The following issues may have already been fixed in the newer releases.
- 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.
- has_meta_json
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Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- meta_yml_has_provides
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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.
- has_security_doc
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Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
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Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
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Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
Modules
| 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 |