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Andrew Page > Bio-Roary-3.10.0

Bio-Roary-3.10.0

This Release Bio-Roary-3.10.0  [Download] [Browse 07 Sep 2017
Latest Release Bio-Roary-3.10.2  [Download] [Browse 08 Sep 2017
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Repository https://github.com/sanger-pathogens/Roary.git
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License The GNU General Public License, Version not specified
Special Files
AUTHORS
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::Roary Create a pan genome     3.10.0
Bio::Roary::AccessoryBinaryFasta Output a FASTA file which represents the binary presence and absence of genes in the accessory genome     3.10.0
Bio::Roary::AccessoryClustering Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters     3.10.0
Bio::Roary::AnalyseGroups Take in a groups file and the original FASTA files and create plots and stats     3.10.0
Bio::Roary::AnnotateGroups Take in a group file and associated GFF files for the isolates and update the group name to the gene name     3.10.0
Bio::Roary::AssemblyStatistics Given a spreadsheet of gene presence and absence calculate some statistics     3.10.0
Bio::Roary::BedFromGFFRole A role to create a bed file from a gff     3.10.0
Bio::Roary::ChunkFastaFile Take in a FASTA file and chunk it up into smaller pieces.     3.10.0
Bio::Roary::ClustersRole A role to read a clusters file from CD hit     3.10.0
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     3.10.0
Bio::Roary::CommandLine::AssemblyStatistics Given a spreadsheet of gene presence and absence calculate some statistics     3.10.0
Bio::Roary::CommandLine::Common Common command line settings     3.10.0
Bio::Roary::CommandLine::CreatePanGenome Take in FASTA files of proteins and cluster them     3.10.0
Bio::Roary::CommandLine::ExtractProteomeFromGff Take in GFF files and output the proteome     3.10.0
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides Take in a multifasta file of nucleotides, convert to proteins and align with PRANK     3.10.0
Bio::Roary::CommandLine::IterativeCdhit Iteratively run cdhit     3.10.0
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp Take in a FASTA file of proteins and blast against itself     3.10.0
Bio::Roary::CommandLine::QueryRoary Take in a groups file and the protein fasta files and output selected data     3.10.0
Bio::Roary::CommandLine::Roary Take in FASTA files of proteins and cluster them     3.10.0
Bio::Roary::CommandLine::RoaryCoreAlignment Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.     3.10.0
Bio::Roary::CommandLine::RoaryPostAnalysis Perform the post analysis on the pan genome     3.10.0
Bio::Roary::CommandLine::RoaryReorderSpreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet     3.10.0
Bio::Roary::CommandLine::TransferAnnotationToGroups Take in a groups file and a set of GFF files and transfer the consensus annotation     3.10.0
Bio::Roary::CommandLine::UniqueGenesPerSample Take in the clustered file and produce a sorted file with the frequency of each samples unique genes     3.10.0
Bio::Roary::ContigsToGeneIDsFromGFF Parse a GFF and efficiently and extract ordered gene ids on each contig     3.10.0
Bio::Roary::Exceptions Exceptions for input data     3.10.0
Bio::Roary::External::Blastp Wrapper around NCBIs blastp command     3.10.0
Bio::Roary::External::Cdhit Wrapper to run cd-hit     3.10.0
Bio::Roary::External::CheckTools Check external executables are available and are the correct version     3.10.0
Bio::Roary::External::Fasttree Wrapper to run Fasttree     3.10.0
Bio::Roary::External::GeneAlignmentFromNucleotides Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT     3.10.0
Bio::Roary::External::IterativeCdhit Iteratively run CDhit     3.10.0
Bio::Roary::External::Mafft Wrapper to run mafft     3.10.0
Bio::Roary::External::Makeblastdb Wrapper around NCBIs makeblastdb command     3.10.0
Bio::Roary::External::Mcl Wrapper around MCL which takes in blast results and outputs clustered results     3.10.0
Bio::Roary::External::PostAnalysis Perform the post analysis     3.10.0
Bio::Roary::External::Prank Wrapper to run prank     3.10.0
Bio::Roary::ExtractCoreGenesFromSpreadsheet Take in a spreadsheet produced by the pipeline and identify the core genes.     3.10.0
Bio::Roary::ExtractProteomeFromGFF Take in a GFF file and create protein sequences in FASTA format     3.10.0
Bio::Roary::ExtractProteomeFromGFFs Take in GFF files and create protein sequences in FASTA format     3.10.0
Bio::Roary::FilterFullClusters Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters     3.10.0
Bio::Roary::FilterUnknownsFromFasta Take in fasta files, remove sequences with too many unknowns and return a list of the new files     3.10.0
Bio::Roary::GeneNamesFromGFF Parse a GFF and efficiently extract ID -> Gene Name     3.10.0
Bio::Roary::GroupLabels Add labels to the groups     3.10.0
Bio::Roary::GroupStatistics Add labels to the groups     3.10.0
Bio::Roary::InflateClusters Take the clusters file from cd-hit and use it to inflate the output of MCL     3.10.0
Bio::Roary::IterativeCdhit Run CDhit iteratively with reducing thresholds, removing full clusters each time     3.10.0
Bio::Roary::JobRunner::Local Execute a set of commands locally     3.10.0
Bio::Roary::JobRunner::Parallel Use GNU Parallel     3.10.0
Bio::Roary::JobRunner::Role A role to add job runner functionality     3.10.0
Bio::Roary::LookupGeneFiles Take in an ordering of genes and a directory and return an ordered list of file locations     3.10.0
Bio::Roary::MergeMultifastaAlignments Merge multifasta alignment files with equal numbers of sequences.     3.10.0
Bio::Roary::OrderGenes Take in GFF files and create a matrix of what genes are beside what other genes     3.10.0
Bio::Roary::Output::BlastIdentityFrequency Take in blast results and find the percentage identity graph     3.10.0
Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL Create an embl file for the header with locations of where genes are in the multifasta alignment of core genes     3.10.0
Bio::Roary::Output::DifferenceBetweenSets Given two sets of isolates and a group file, output whats unique in each and whats in common     3.10.0
Bio::Roary::Output::EMBLHeaderCommon a role containing some common methods for embl header files     3.10.0
Bio::Roary::Output::EmblGroups Create a tab/embl file with the features for drawing pretty pictures     3.10.0
Bio::Roary::Output::GroupMultifasta Take in a group and create a multifasta file     3.10.0
Bio::Roary::Output::GroupsMultifastaNucleotide Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences.     3.10.0
Bio::Roary::Output::GroupsMultifastaProtein Take a multifasta nucleotide file and output it as proteins.     3.10.0
Bio::Roary::Output::GroupsMultifastas Take in a list of groups and create multifastas files for each group     3.10.0
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.     3.10.0
Bio::Roary::Output::NumberOfGroups Create raw output files of group counts for turning into plots     3.10.0
Bio::Roary::Output::QueryGroups Output the groups of the union of a set of input isolates     3.10.0
Bio::Roary::ParallelAllAgainstAllBlast Run all against all blast in parallel     3.10.0
Bio::Roary::ParseGFFAnnotationRole A role for parsing a gff file efficiently     3.10.0
Bio::Roary::PostAnalysis Post analysis of pan genomes     3.10.0
Bio::Roary::PrepareInputFiles Take in a mixture of FASTA and GFF input files and output FASTA proteomes only     3.10.0
Bio::Roary::PresenceAbsenceMatrix Create a matrix with presence and absence     3.10.0
Bio::Roary::QC::Report generate a report based on kraken output     3.10.0
Bio::Roary::ReformatInputGFFs Take in gff files and add suffix where a gene id is seen twice     3.10.0
Bio::Roary::ReorderSpreadsheet Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns     3.10.0
Bio::Roary::SampleOrder Take in a tree file and return an ordering of the samples     3.10.0
Bio::Roary::SequenceLengths Take in a fasta file and create a hash with the length of each sequence     3.10.0
Bio::Roary::SortFasta sort a fasta file by name     3.10.0
Bio::Roary::SplitGroups split groups     3.10.0
Bio::Roary::SpreadsheetRole Read and write a spreadsheet     3.10.0
Bio::Roary::UniqueGenesPerSample Take in the clustered file and produce a sorted file with the frequency of each samples unique genes     3.10.0

Documentation

create_pan_genome Create a pan genome from a set of GFF files with WTSI defaults  
extract_proteome_from_gff Take in GFF files and output the proteome  
iterative_cdhit Iteratively run cdhit  
pan_genome_assembly_statistics Given a spreadsheet of gene presence and absence calculate some statistics  
pan_genome_core_alignment Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.  
pan_genome_post_analysis Perform the post analysis on the pan genome  
pan_genome_reorder_spreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet  
parallel_all_against_all_blastp Take in a FASTA file of proteins and blast against itself  
protein_alignment_from_nucleotides Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT  
query_pan_genome Take in a groups file and the protein fasta files and output selected data  
roary Create a pan genome from a set of GFF files  
roary-unique_genes_per_sample Take in the clustered file and produce a sorted file with the frequency of each samples unique genes  
transfer_annotation_to_groups Take in a groups file and a set of GFF files and transfer the consensus annotation  

Other Files

README.md