# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.008.
AUTHORS
CITATIONS.md
Dockerfile
GPL-LICENSE
LICENSE
MANIFEST
META.json
META.yml
Makefile.PL
README
README.md
bin/download_fasta_database
bin/download_mlst_databases
bin/get_emm_sequence_type
bin/get_sequence_type
dist.ini
example/README.md
example/expected_output_data/concatenated_alleles.fa
example/expected_output_data/mlst_results.allele.csv
example/expected_output_data/mlst_results.genomic.csv
example/input_data/Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1.fa
example/input_data/Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1.fa
example/input_data/Salmonella_enterica_subsp_enterica_serovar_Weltevreden_str_10259_v0.2.fa
example/mlst_databases/Salmonella_enterica/alleles/aroC.tfa
example/mlst_databases/Salmonella_enterica/alleles/dnaN.tfa
example/mlst_databases/Salmonella_enterica/alleles/hemD.tfa
example/mlst_databases/Salmonella_enterica/alleles/hisD.tfa
example/mlst_databases/Salmonella_enterica/alleles/purE.tfa
example/mlst_databases/Salmonella_enterica/alleles/sucA.tfa
example/mlst_databases/Salmonella_enterica/alleles/thrA.tfa
example/mlst_databases/Salmonella_enterica/profiles/senterica.txt
install_dependencies.sh
lib/Bio/MLST/Blast/BlastN.pm
lib/Bio/MLST/Blast/Database.pm
lib/Bio/MLST/CDC/Convert.pm
lib/Bio/MLST/Check.pm
lib/Bio/MLST/CheckMultipleSpecies.pm
lib/Bio/MLST/CompareAlleles.pm
lib/Bio/MLST/DatabaseSettings.pm
lib/Bio/MLST/Databases.pm
lib/Bio/MLST/Download/Database.pm
lib/Bio/MLST/Download/Databases.pm
lib/Bio/MLST/Download/Downloadable.pm
lib/Bio/MLST/FilterAlleles.pm
lib/Bio/MLST/NormaliseFasta.pm
lib/Bio/MLST/OutputFasta.pm
lib/Bio/MLST/ProcessFasta.pm
lib/Bio/MLST/SearchForFiles.pm
lib/Bio/MLST/SequenceType.pm
lib/Bio/MLST/Spreadsheet/File.pm
lib/Bio/MLST/Spreadsheet/Row.pm
lib/Bio/MLST/Types.pm
lib/Bio/MLST/Validate/Executable.pm
lib/Bio/MLST/Validate/File.pm
lib/Bio/MLST/Validate/Resource.pm
paper.bib
paper.md
t/00-report-prereqs.dd
t/00-report-prereqs.t
t/Blast/BlastN.t
t/Blast/Database.t
t/CDC/Convert.t
t/Download/Database.t
t/Download/Database_fails.t
t/Download/Database_succeeds.t
t/Download/Databases.t
t/FilterAlleles.t
t/Input/NormaliseFasta.t
t/Output/Databases.t
t/Output/MultipleFastas.t
t/Output/MultipleSpecies.t
t/Output/OutputFasta.t
t/Output/SpreadsheetRow.t
t/SequenceTypes/CompareAlleles.t
t/SequenceTypes/SearchForFiles.t
t/SequenceTypes/SequenceType.t
t/Settings/DatabaseSettings.t
t/Validate/Executable.t
t/data/CDC_emmST_partial.tfa
t/data/Pediococcus_pentosaceus_filtering.xml
t/data/Streptococcus_pyogenes_emmST_contigs.fa
t/data/Streptococcus_pyogenes_emmST_unknown.fa
t/data/abc.fas
t/data/adk.tfa
t/data/adk_99_percent.tfa
t/data/adk_contamination.tfa
t/data/adk_imperfect.tfa
t/data/adk_imperfect_contamination.tfa
t/data/adk_less_than_95_percent.tfa
t/data/adk_top_hit_low_hit.tfa
t/data/adk_truncation.tfa
t/data/adk_two_imperfect_contamination.tfa
t/data/bbb.fas
t/data/bordetella.txt
t/data/ccc.fas
t/data/contigs.fa
t/data/contigs_check_concat_allele_order.fa
t/data/contigs_missing_locus.fa
t/data/contigs_near_match.fa
t/data/contigs_novel.fa
t/data/contigs_one_unknown.tfa
t/data/contigs_pipe_character_in_seq_name.fa
t/data/databases/Escherichia_coli_1/alleles/adk.tfa
t/data/databases/Escherichia_coli_1/alleles/purA.tfa
t/data/databases/Escherichia_coli_1/alleles/recA.tfa
t/data/databases/Escherichia_coli_1/profiles/escherichia_coli.txt
t/data/databases/Helicobacter_pylori/alleles/atpA.tfa
t/data/databases/Helicobacter_pylori/alleles/efp.tfa
t/data/databases/Helicobacter_pylori/alleles/mutY.tfa
t/data/databases/Helicobacter_pylori/profiles/hpylori.txt
t/data/databases/Streptococcus_pyogenes/profiles/spyogenes.txt
t/data/databases/Streptococcus_pyogenes_emmST/alleles/emmST.tfa
t/data/databases/Streptococcus_pyogenes_emmST/profiles/Streptococcus_pyogenes_emmST.txt
t/data/ddd.fas
t/data/eee.fas
t/data/efg.fas
t/data/expected_Streptococcus_pyogenes_emmST.allele.csv
t/data/expected_Streptococcus_pyogenes_emmST.genomic.csv
t/data/expected_Streptococcus_pyogenes_emmST_alleles.fa
t/data/expected_Streptococcus_pyogenes_emmST_alleles_with_unknown.fa
t/data/expected_concatenated_alleles.fa
t/data/expected_mlst_results.allele.csv
t/data/expected_mlst_results.genomic.csv
t/data/expected_multi_mlst_results.allele.csv
t/data/expected_multi_mlst_results.genomic.csv
t/data/expected_sorted_concatenated_alleles.fa
t/data/expected_sorted_mlst_results.allele.csv
t/data/expected_sorted_mlst_results.genomic.csv
t/data/expected_three_concatenated_alleles.fa
t/data/expected_three_concatenated_alleles.phylip
t/data/expected_three_contigs_one_unknown.unknown_allele.adk-2~.fa
t/data/expected_three_contigs_one_unknown.unknown_allele.recA-1~.fa
t/data/expected_three_mlst_best_results.allele.csv
t/data/expected_three_mlst_best_results.genomic.csv
t/data/expected_three_mlst_results.allele.csv
t/data/expected_three_mlst_results.genomic.csv
t/data/expected_two_concatenated_alleles.fa
t/data/expected_two_mlst_results.allele.csv
t/data/expected_two_mlst_results.genomic.csv
t/data/fake_executables/another_executable.sh
t/data/fake_executables/executable.sh
t/data/fake_executables/not_executable.sh
t/data/gdh_fake_blast_output.sh
t/data/homo_sapiens.txt
t/data/missing_web_database.xml
t/data/overall_databases.xml
t/data/purA.tfa
t/data/recA.tfa
t/requires_external.t
weaver.ini
xt/author/00-compile.t
xt/author/pod-syntax.t