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LICENSE
MANIFEST
META.yml
Makefile.PL
README
README.md
bin/bacteria_assembly_and_annotation
bin/bacteria_assembly_single_cell
bin/bacteria_mapping
bin/bacteria_register_and_qc_study
bin/bacteria_rna_seq_expression
bin/bacteria_snp_calling
bin/eukaryote_assembly
bin/eukaryote_mapping
bin/eukaryote_register_and_qc_study
bin/eukaryote_rna_seq_expression
bin/eukaryote_snp_calling
bin/helminth_mapping
bin/helminth_register_and_qc_study
bin/helminth_rna_seq_expression
bin/helminth_snp_calling
bin/setup_global_configs
bin/virus_assembly_and_annotation
bin/virus_mapping
bin/virus_register_and_qc_study
bin/virus_rna_seq_expression
bin/virus_snp_calling
dist.ini
lib/Bio/VertRes/Config.pm
lib/Bio/VertRes/Config/CommandLine/BacteriaAssemblyAndAnnotation.pm
lib/Bio/VertRes/Config/CommandLine/BacteriaAssemblySingleCell.pm
lib/Bio/VertRes/Config/CommandLine/BacteriaMapping.pm
lib/Bio/VertRes/Config/CommandLine/BacteriaRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/CommandLine/BacteriaRnaSeqExpression.pm
lib/Bio/VertRes/Config/CommandLine/BacteriaSnpCalling.pm
lib/Bio/VertRes/Config/CommandLine/Common.pm
lib/Bio/VertRes/Config/CommandLine/ConstructLimits.pm
lib/Bio/VertRes/Config/CommandLine/EukaryotesAssembly.pm
lib/Bio/VertRes/Config/CommandLine/EukaryotesMapping.pm
lib/Bio/VertRes/Config/CommandLine/EukaryotesRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/CommandLine/EukaryotesRnaSeqExpression.pm
lib/Bio/VertRes/Config/CommandLine/EukaryotesSnpCalling.pm
lib/Bio/VertRes/Config/CommandLine/HelminthMapping.pm
lib/Bio/VertRes/Config/CommandLine/HelminthRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/CommandLine/HelminthRnaSeqExpression.pm
lib/Bio/VertRes/Config/CommandLine/HelminthSnpCalling.pm
lib/Bio/VertRes/Config/CommandLine/LogParameters.pm
lib/Bio/VertRes/Config/CommandLine/ReferenceHandlingRole.pm
lib/Bio/VertRes/Config/CommandLine/StudyNameSearch.pm
lib/Bio/VertRes/Config/CommandLine/VirusAssemblyAndAnnotation.pm
lib/Bio/VertRes/Config/CommandLine/VirusMapping.pm
lib/Bio/VertRes/Config/CommandLine/VirusRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/CommandLine/VirusRnaSeqExpression.pm
lib/Bio/VertRes/Config/CommandLine/VirusSnpCalling.pm
lib/Bio/VertRes/Config/Exceptions.pm
lib/Bio/VertRes/Config/MultipleTopLevelFiles.pm
lib/Bio/VertRes/Config/Pipelines/AnnotateAssembly.pm
lib/Bio/VertRes/Config/Pipelines/Assembly.pm
lib/Bio/VertRes/Config/Pipelines/BamImprovement.pm
lib/Bio/VertRes/Config/Pipelines/Bowtie2Mapping.pm
lib/Bio/VertRes/Config/Pipelines/BwaMapping.pm
lib/Bio/VertRes/Config/Pipelines/Common.pm
lib/Bio/VertRes/Config/Pipelines/Import.pm
lib/Bio/VertRes/Config/Pipelines/Mapping.pm
lib/Bio/VertRes/Config/Pipelines/QC.pm
lib/Bio/VertRes/Config/Pipelines/RnaSeqExpression.pm
lib/Bio/VertRes/Config/Pipelines/Roles/FilenameWithReference.pm
lib/Bio/VertRes/Config/Pipelines/Roles/MetaDataFilter.pm
lib/Bio/VertRes/Config/Pipelines/Roles/MultiplePrefix.pm
lib/Bio/VertRes/Config/Pipelines/Roles/RootDatabaseLookup.pm
lib/Bio/VertRes/Config/Pipelines/SmaltMapping.pm
lib/Bio/VertRes/Config/Pipelines/SnpCalling.pm
lib/Bio/VertRes/Config/Pipelines/SpadesAssembly.pm
lib/Bio/VertRes/Config/Pipelines/Ssaha2Mapping.pm
lib/Bio/VertRes/Config/Pipelines/StampyMapping.pm
lib/Bio/VertRes/Config/Pipelines/Store.pm
lib/Bio/VertRes/Config/Pipelines/TophatMapping.pm
lib/Bio/VertRes/Config/Pipelines/Tradis.pm
lib/Bio/VertRes/Config/Pipelines/VelvetAssembly.pm
lib/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.pm
lib/Bio/VertRes/Config/Recipes/BacteriaAssemblySingleCell.pm
lib/Bio/VertRes/Config/Recipes/BacteriaMappingUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/BacteriaMappingUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/BacteriaMappingUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/BacteriaMappingUsingSsaha2.pm
lib/Bio/VertRes/Config/Recipes/BacteriaMappingUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/BacteriaMappingUsingTophat.pm
lib/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingTophat.pm
lib/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSsaha2.pm
lib/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/Common.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesAssembly.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSsaha2.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingTophat.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpressionUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpressionUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpressionUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpressionUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpressionUsingTophat.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSsaha2.pm
lib/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/Global.pm
lib/Bio/VertRes/Config/Recipes/HelminthRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/Recipes/Roles/BacteriaMapping.pm
lib/Bio/VertRes/Config/Recipes/Roles/BacteriaRegisterStudy.pm
lib/Bio/VertRes/Config/Recipes/Roles/BacteriaRnaSeqExpression.pm
lib/Bio/VertRes/Config/Recipes/Roles/BacteriaSnpCalling.pm
lib/Bio/VertRes/Config/Recipes/Roles/CreateGlobal.pm
lib/Bio/VertRes/Config/Recipes/Roles/EukaryotesMapping.pm
lib/Bio/VertRes/Config/Recipes/Roles/EukaryotesRegisterStudy.pm
lib/Bio/VertRes/Config/Recipes/Roles/EukaryotesRnaSeqExpression.pm
lib/Bio/VertRes/Config/Recipes/Roles/EukaryotesSnpCalling.pm
lib/Bio/VertRes/Config/Recipes/Roles/Reference.pm
lib/Bio/VertRes/Config/Recipes/Roles/RegisterStudy.pm
lib/Bio/VertRes/Config/Recipes/Roles/VirusMapping.pm
lib/Bio/VertRes/Config/Recipes/Roles/VirusRegisterStudy.pm
lib/Bio/VertRes/Config/Recipes/Roles/VirusRnaSeqExpression.pm
lib/Bio/VertRes/Config/Recipes/Roles/VirusSnpCalling.pm
lib/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.pm
lib/Bio/VertRes/Config/Recipes/VirusMappingUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/VirusMappingUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/VirusMappingUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/VirusMappingUsingSsaha2.pm
lib/Bio/VertRes/Config/Recipes/VirusMappingUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/VirusMappingUsingTophat.pm
lib/Bio/VertRes/Config/Recipes/VirusRegisterAndQCStudy.pm
lib/Bio/VertRes/Config/Recipes/VirusRnaSeqExpressionUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/VirusRnaSeqExpressionUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/VirusRnaSeqExpressionUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/VirusRnaSeqExpressionUsingStampy.pm
lib/Bio/VertRes/Config/Recipes/VirusRnaSeqExpressionUsingTophat.pm
lib/Bio/VertRes/Config/Recipes/VirusSnpCallingUsingBowtie2.pm
lib/Bio/VertRes/Config/Recipes/VirusSnpCallingUsingBwa.pm
lib/Bio/VertRes/Config/Recipes/VirusSnpCallingUsingSmalt.pm
lib/Bio/VertRes/Config/Recipes/VirusSnpCallingUsingSsaha2.pm
lib/Bio/VertRes/Config/Recipes/VirusSnpCallingUsingStampy.pm
lib/Bio/VertRes/Config/References.pm
lib/Bio/VertRes/Config/RegisterStudy.pm
lib/Bio/VertRes/Config/TopLevel.pm
lib/Bio/VertRes/Config/Types.pm
lib/Bio/VertRes/Config/Validate/File.pm
lib/Bio/VertRes/Config/Validate/Prefix.pm
software_license
t/Bio/VertRes/Config/CommandLine/Common.t
t/Bio/VertRes/Config/CommandLine/ConstructLimits.t
t/Bio/VertRes/Config/CommandLine/LogParameters.t
t/Bio/VertRes/Config/CommandLine/StudyNameSearch.t
t/Bio/VertRes/Config/MultipleTopLevelFiles.t
t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t
t/Bio/VertRes/Config/Pipelines/Assembly.t
t/Bio/VertRes/Config/Pipelines/BamImprovement.t
t/Bio/VertRes/Config/Pipelines/Bowtie2Mapping.t
t/Bio/VertRes/Config/Pipelines/BwaMapping.t
t/Bio/VertRes/Config/Pipelines/Common.t
t/Bio/VertRes/Config/Pipelines/Import.t
t/Bio/VertRes/Config/Pipelines/Mapping.t
t/Bio/VertRes/Config/Pipelines/QC.t
t/Bio/VertRes/Config/Pipelines/RnaSeqExpression.t
t/Bio/VertRes/Config/Pipelines/SmaltMapping.t
t/Bio/VertRes/Config/Pipelines/SnpCalling.t
t/Bio/VertRes/Config/Pipelines/SpadesAssembly.t
t/Bio/VertRes/Config/Pipelines/Ssaha2Mapping.t
t/Bio/VertRes/Config/Pipelines/StampyMapping.t
t/Bio/VertRes/Config/Pipelines/Store.t
t/Bio/VertRes/Config/Pipelines/Tradis.t
t/Bio/VertRes/Config/Pipelines/VelvetAssembly.t
t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t
t/Bio/VertRes/Config/Recipes/BacteriaAssemblySingleCell.t
t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBwa.t
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingSmalt.t
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBwa.t
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSmalt.t
t/Bio/VertRes/Config/Recipes/EukaryotesAssembly.t
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBwa.t
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSmalt.t
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSsaha2.t
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingStampy.t
t/Bio/VertRes/Config/Recipes/EukaryotesRegisterAndQCStudy.t
t/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpression.t
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBwa.t
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSmalt.t
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSsaha2.t
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.t
t/Bio/VertRes/Config/Recipes/Global.t
t/Bio/VertRes/Config/Recipes/HelminthRegisterAndQCStudy.t
t/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.t
t/Bio/VertRes/Config/Recipes/VirusRegisterAndQCStudy.t
t/Bio/VertRes/Config/References.t
t/Bio/VertRes/Config/RegisterStudy.t
t/Bio/VertRes/Config/TopLevel.t
t/bin/bacteria_assembly_and_annotation.t
t/bin/bacteria_assembly_single_cell.t
t/bin/bacteria_mapping.t
t/bin/bacteria_register_and_qc_study.t
t/bin/bacteria_rna_seq_expression.t
t/bin/bacteria_snp_calling.t
t/bin/eukaryote_assembly.t
t/bin/eukaryote_mapping.t
t/bin/eukaryote_register_and_qc_study.t
t/bin/eukaryote_rna_seq_expression.t
t/bin/eukaryote_snp_calling.t
t/bin/helminth_mapping.t
t/bin/helminth_register_and_qc_study.t
t/bin/helminth_rna_seq_expression.t
t/bin/helminth_snp_calling.t
t/bin/log_parameters.t
t/bin/setup_global_configs.t
t/bin/virus_assembly_and_annotation.t
t/bin/virus_mapping.t
t/bin/virus_register_and_qc_study.t
t/bin/virus_rna_seq_expression.t
t/bin/virus_snp_calling.t
t/data/constructlimits_lanes
t/data/database_connection_details
t/data/lanes_file
t/data/refs.index
t/lib/TestHelper.pm
weaver.ini