📦 roary

95 pages

B

Bio::Roary(3pm)Create a pan genome✨
Bio::Roary::AccessoryBinaryFasta(3pm)Output a FASTA file which represents the binary presence and absence of genes in the accessory genome✨
Bio::Roary::AccessoryClustering(3pm)Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters✨
Bio::Roary::AnalyseGroups(3pm)Take in a groups file and the original FASTA files and create plots and stats✨
Bio::Roary::AnnotateGroups(3pm)Take in a group file and associated GFF files for the isolates and update the group name to the gene name✨
Bio::Roary::AssemblyStatistics(3pm)Given a spreadsheet of gene presence and absence calculate some statistics✨
Bio::Roary::BedFromGFFRole(3pm)A role to create a bed file from a gff✨
Bio::Roary::ChunkFastaFile(3pm)Take in a FASTA file and chunk it up into smaller pieces.✨
Bio::Roary::ClustersRole(3pm)A role to read a clusters file from CD hit✨
Bio::Roary::CombinedProteome(3pm)Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's✨
Bio::Roary::CommandLine::AssemblyStatistics(3pm)Given a spreadsheet of gene presence and absence calculate some statistics✨
Bio::Roary::CommandLine::Common(3pm)Common command line settings✨
Bio::Roary::CommandLine::CreatePanGenome(3pm)Take in FASTA files of proteins and cluster them✨
Bio::Roary::CommandLine::ExtractProteomeFromGff(3pm)Take in GFF files and output the proteome✨
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides(3pm)Take in a multifasta file of nucleotides, convert to proteins and align with PRANK✨
Bio::Roary::CommandLine::IterativeCdhit(3pm)Iteratively run cdhit✨
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp(3pm)Take in a FASTA file of proteins and blast against itself✨
Bio::Roary::CommandLine::QueryRoary(3pm)Take in a groups file and the protein fasta files and output selected data✨
Bio::Roary::CommandLine::Roary(3pm)Take in FASTA files of proteins and cluster them✨
Bio::Roary::CommandLine::RoaryCoreAlignment(3pm)Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.✨
Bio::Roary::CommandLine::RoaryPostAnalysis(3pm)Perform the post analysis on the pan genome✨
Bio::Roary::CommandLine::RoaryReorderSpreadsheet(3pm)Take in a tree and a spreadsheet and output a reordered spreadsheet✨
Bio::Roary::CommandLine::TransferAnnotationToGroups(3pm)Take in a groups file and a set of GFF files and transfer the consensus annotation✨
Bio::Roary::CommandLine::UniqueGenesPerSample(3pm)Take in the clustered file and produce a sorted file with the frequency of each samples unique genes✨
Bio::Roary::ContigsToGeneIDsFromGFF(3pm)Parse a GFF and efficiently and extract ordered gene ids on each contig✨
Bio::Roary::Exceptions(3pm)Exceptions for input data✨
Bio::Roary::External::Blastp(3pm)Wrapper around NCBIs blastp command✨
Bio::Roary::External::Cdhit(3pm)Wrapper to run cd-hit✨
Bio::Roary::External::CheckTools(3pm)Check external executables are available and are the correct version✨
Bio::Roary::External::Fasttree(3pm)Wrapper to run Fasttree✨
Bio::Roary::External::GeneAlignmentFromNucleotides(3pm)Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT✨
Bio::Roary::External::IterativeCdhit(3pm)Iteratively run CDhit✨
Bio::Roary::External::Mafft(3pm)Wrapper to run mafft✨
Bio::Roary::External::Makeblastdb(3pm)Wrapper around NCBIs makeblastdb command✨
Bio::Roary::External::Mcl(3pm)Wrapper around MCL which takes in blast results and outputs clustered results✨
Bio::Roary::External::PostAnalysis(3pm)Perform the post analysis✨
Bio::Roary::External::Prank(3pm)Wrapper to run prank✨
Bio::Roary::ExtractCoreGenesFromSpreadsheet(3pm)Take in a spreadsheet produced by the pipeline and identify the core genes.✨
Bio::Roary::ExtractProteomeFromGFF(3pm)Take in a GFF file and create protein sequences in FASTA format✨
Bio::Roary::ExtractProteomeFromGFFs(3pm)Take in GFF files and create protein sequences in FASTA format✨
Bio::Roary::FilterFullClusters(3pm)Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters✨
Bio::Roary::FilterUnknownsFromFasta(3pm)Take in fasta files, remove sequences with too many unknowns and return a list of the new files✨
Bio::Roary::GeneNamesFromGFF(3pm)Parse a GFF and efficiently extract ID -> Gene Name✨
Bio::Roary::GroupLabels(3pm)Add labels to the groups✨
Bio::Roary::GroupStatistics(3pm)Add labels to the groups✨
Bio::Roary::InflateClusters(3pm)Take the clusters file from cd-hit and use it to inflate the output of MCL✨
Bio::Roary::IterativeCdhit(3pm)Run CDhit iteratively with reducing thresholds, removing full clusters each time✨
Bio::Roary::JobRunner::Local(3pm)Execute a set of commands locally✨
Bio::Roary::JobRunner::Parallel(3pm)Use GNU Parallel✨
Bio::Roary::JobRunner::Role(3pm)A role to add job runner functionality✨
Bio::Roary::LookupGeneFiles(3pm)Take in an ordering of genes and a directory and return an ordered list of file locations✨
Bio::Roary::MergeMultifastaAlignments(3pm)Merge multifasta alignment files with equal numbers of sequences.✨
Bio::Roary::OrderGenes(3pm)Take in GFF files and create a matrix of what genes are beside what other genes✨
Bio::Roary::Output::BlastIdentityFrequency(3pm)Take in blast results and find the percentage identity graph✨
Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL(3pm)Create an embl file for the header with locations of where genes are in the multifasta alignment of core genes✨
Bio::Roary::Output::DifferenceBetweenSets(3pm)Given two sets of isolates and a group file, output whats unique in each and whats in common✨
Bio::Roary::Output::EmblGroups(3pm)Create a tab/embl file with the features for drawing pretty pictures✨
Bio::Roary::Output::EMBLHeaderCommon(3pm)a role containing some common methods for embl header files✨
Bio::Roary::Output::GroupMultifasta(3pm)Take in a group and create a multifasta file✨
Bio::Roary::Output::GroupsMultifastaNucleotide(3pm)Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences.✨
Bio::Roary::Output::GroupsMultifastaProtein(3pm)Take a multifasta nucleotide file and output it as proteins.✨
Bio::Roary::Output::GroupsMultifastas(3pm)Take in a list of groups and create multifastas files for each group✨
Bio::Roary::Output::GroupsMultifastasNucleotide(3pm)Take in a set of GFF files and a groups file and output one multifasta file per group with nucleotide sequences.✨
Bio::Roary::Output::NumberOfGroups(3pm)Create raw output files of group counts for turning into plots✨
Bio::Roary::Output::QueryGroups(3pm)Output the groups of the union of a set of input isolates✨
Bio::Roary::ParallelAllAgainstAllBlast(3pm)Run all against all blast in parallel✨
Bio::Roary::ParseGFFAnnotationRole(3pm)A role for parsing a gff file efficiently✨
Bio::Roary::PostAnalysis(3pm)Post analysis of pan genomes✨
Bio::Roary::PrepareInputFiles(3pm)Take in a mixture of FASTA and GFF input files and output FASTA proteomes only✨
Bio::Roary::PresenceAbsenceMatrix(3pm)Create a matrix with presence and absence✨
Bio::Roary::QC::Report(3pm)generate a report based on kraken output✨
Bio::Roary::ReformatInputGFFs(3pm)Take in gff files and add suffix where a gene id is seen twice✨
Bio::Roary::ReorderSpreadsheet(3pm)Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns✨
Bio::Roary::SampleOrder(3pm)Take in a tree file and return an ordering of the samples✨
Bio::Roary::SequenceLengths(3pm)Take in a fasta file and create a hash with the length of each sequence✨
Bio::Roary::SortFasta(3pm)sort a fasta file by name✨
Bio::Roary::SplitGroups(3pm)split groups✨
Bio::Roary::SpreadsheetRole(3pm)Read and write a spreadsheet✨
Bio::Roary::UniqueGenesPerSample(3pm)Take in the clustered file and produce a sorted file with the frequency of each samples unique genes✨

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create_pan_genome(1p)Create a pan genome from a set of GFF files with WTSI defaults✨
create_pan_genome_plots(1p)Create R plots✨

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extract_proteome_from_gff(1p)Take in GFF files and output the proteome✨

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iterative_cdhit(1p)Iteratively run cdhit✨

P

pan_genome_assembly_statistics(1p)Given a spreadsheet of gene presence and absence calculate some statistics✨
pan_genome_core_alignment(1p)Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.✨
pan_genome_post_analysis(1p)Perform the post analysis on the pan genome✨
pan_genome_reorder_spreadsheet(1p)Take in a tree and a spreadsheet and output a reordered spreadsheet✨
parallel_all_against_all_blastp(1p)Take in a FASTA file of proteins and blast against itself✨
protein_alignment_from_nucleotides(1p)Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT✨

Q

query_pan_genome(1p)Take in a groups file and the protein fasta files and output selected data✨

R

roary(1p)Create a pan genome from a set of GFF files✨
roary-pan_genome_reorder_spreadsheet(1p)Take in a tree and a spreadsheet and output a reordered spreadsheet✨
roary-query_pan_genome(1p)Take in a groups file and the protein fasta files and output selected data✨
roary-unique_genes_per_sample(1p)Take in the clustered file and produce a sorted file with the frequency of each samples unique genes✨

T

transfer_annotation_to_groups(1p)Take in a groups file and a set of GFF files and transfer the consensus annotation✨