Files in phac-nml/wade
Executes molecular typing on contig assemblies
.Rbuildignore
.gitignore
.gitmodules
DESCRIPTION
LICENSE
NAMESPACE
PackageInstaller.R
R/16SrRNA.R
R/23SrRNA.R
R/CommonFunctions.R
R/EMM.R
R/EMM2.R
R/FindDuplicates.R
R/LabwareUpload_GAS_AMR.R
R/LabwareUpload_GAS_TOXINS.R
R/LabwareUpload_GBS_AMR.R
R/LabwareUpload_GONO_AMR.R
R/LabwareUpload_Metrics.R
R/LabwareUpload_PNEUMO_AMR.R
R/LabwareUpload_PNEUMO_VIRULENCE.R
R/MASTER.R
R/MIC_Compare.R
R/MLST.R
R/Makeblastdb.R
R/Newick_sort_order.R
R/Proximity_Test.R
R/Remove_Duplicates_fasta.R
R/Rename_Submitted.R
R/SerotypeR.R
R/UpdateLookups.R
README.md
WADE.R
WADE.Rproj
WADE/DirectoryLocations.csv
WADE/Example_contigs/GAS.fasta
WADE/Example_contigs/GBS.fasta
WADE/Example_contigs/GONO.fasta
WADE/Example_contigs/GONO.vcf
WADE/Example_contigs/PNEUMO.fasta
WADE/Example_contigs/PNEUMO.vcf
WADE/Output/empty.txt
WADE/list.csv
WADE/temp/empty.txt
man/EMM_pipeline.Rd
man/MASTER_pipeline.Rd
man/MIC_compare.Rd
man/MLST_pipeline.Rd
man/MakeblastDB_pipeline.Rd
man/Org_id.Rd
man/SEROTYPE_pipeline.Rd
man/buildSNVtable.Rd
man/find_sample_duplicates.Rd
man/getdirectory.Rd
man/labware_gas_amr.Rd
man/labware_gas_toxins.Rd
man/labware_gbs_amr.Rd
man/labware_gono_amr.Rd
man/labware_pneumo_amr.Rd
man/labware_pneumo_virulence.Rd
man/metrics.Rd
man/nwk_rename_samples.Rd
man/nwk_sort_order.Rd
man/proximity_test.Rd
man/rRNA16S_pipeline.Rd
man/rRNA23S_pipeline.Rd
man/remove_duplicates_fasta.Rd
man/rename_contigs.Rd
man/rename_submitted.Rd
man/update_lookups.Rd
standalones/MasterBlastR/MasterBlastR.R
standalones/MasterBlastR/MasterBlastR_Readme.md
standalones/MasterBlastR/blast_evalues.csv
standalones/SerotypeR/SerotypeR.R
standalones/SerotypeR/SerotypeR_Readme.md
standalones/SerotypeR/allele_lkup_dna/06_wciN.fasta
standalones/SerotypeR/allele_lkup_dna/06_wciN_1.fasta
standalones/SerotypeR/allele_lkup_dna/06_wciN_2.fasta
standalones/SerotypeR/allele_lkup_dna/06_wciN_3.fasta
standalones/SerotypeR/allele_lkup_dna/06_wciP.fasta
standalones/SerotypeR/allele_lkup_dna/06_wzy.fasta
standalones/SerotypeR/allele_lkup_dna/10_wcrC.fasta
standalones/SerotypeR/allele_lkup_dna/10_wcrC_10A.fasta
standalones/SerotypeR/allele_lkup_dna/10_wcrC_10B.fasta
standalones/SerotypeR/allele_lkup_dna/10_wcrO.fasta
standalones/SerotypeR/allele_lkup_dna/11_gct.fasta
standalones/SerotypeR/allele_lkup_dna/11_wcjE.fasta
standalones/SerotypeR/allele_lkup_dna/11_wcrL.fasta
standalones/SerotypeR/allele_lkup_dna/11_wcwC.fasta
standalones/SerotypeR/allele_lkup_dna/12_wciI.fasta
standalones/SerotypeR/allele_lkup_dna/15_wchL.fasta
standalones/SerotypeR/allele_lkup_dna/15_wzd.fasta
standalones/SerotypeR/allele_lkup_dna/23_wchA.fasta
standalones/SerotypeR/allele_lkup_dna/23_wzy_23A.fasta
standalones/SerotypeR/allele_lkup_dna/23_wzy_23BF.fasta
standalones/SerotypeR/allele_lkup_dna/24_glf.fasta
standalones/SerotypeR/allele_lkup_dna/25_wcyD.fasta
standalones/SerotypeR/allele_lkup_dna/35_wciG.fasta
standalones/SerotypeR/allele_lkup_dna/reference_CPS.fasta
standalones/SerotypeR/allele_lkup_dna/reference_CPS_with_06G.fasta
standalones/SerotypeR/reference/06_loci.csv
standalones/SerotypeR/reference/06_loci_lookup.csv
standalones/SerotypeR/reference/06_loci_mutations.csv
standalones/SerotypeR/reference/07_loci.csv
standalones/SerotypeR/reference/07_loci_lookup.csv
standalones/SerotypeR/reference/07_loci_mutations.csv
standalones/SerotypeR/reference/09_loci.csv
standalones/SerotypeR/reference/09_loci_lookup.csv
standalones/SerotypeR/reference/09_loci_mutations.csv
standalones/SerotypeR/reference/10_loci.csv
standalones/SerotypeR/reference/10_loci_lookup.csv
standalones/SerotypeR/reference/11_loci.csv
standalones/SerotypeR/reference/11_loci_lookup.csv
standalones/SerotypeR/reference/11_loci_mutations.csv
standalones/SerotypeR/reference/12_loci.csv
standalones/SerotypeR/reference/12_loci_lookup.csv
standalones/SerotypeR/reference/12_loci_mutations.csv
standalones/SerotypeR/reference/15_loci.csv
standalones/SerotypeR/reference/15_loci_lookup.csv
standalones/SerotypeR/reference/18_loci.csv
standalones/SerotypeR/reference/18_loci_lookup.csv
standalones/SerotypeR/reference/19_loci.csv
standalones/SerotypeR/reference/19_loci_lookup.csv
standalones/SerotypeR/reference/22_loci.csv
standalones/SerotypeR/reference/22_loci_lookup.csv
standalones/SerotypeR/reference/23_loci.csv
standalones/SerotypeR/reference/23_loci_lookup.csv
standalones/SerotypeR/reference/24_loci.csv
standalones/SerotypeR/reference/24_loci_lookup.csv
standalones/SerotypeR/reference/24_loci_mutations.csv
standalones/SerotypeR/reference/25_loci.csv
standalones/SerotypeR/reference/25_loci_lookup.csv
standalones/SerotypeR/reference/25_loci_mutations.csv
standalones/SerotypeR/reference/28_loci.csv
standalones/SerotypeR/reference/28_loci_lookup.csv
standalones/SerotypeR/reference/28_loci_mutations.csv
standalones/SerotypeR/reference/32_loci.csv
standalones/SerotypeR/reference/32_loci_lookup.csv
standalones/SerotypeR/reference/33_loci.csv
standalones/SerotypeR/reference/33_loci_lookup.csv
standalones/SerotypeR/reference/35_loci.csv
standalones/SerotypeR/reference/35_loci_lookup.csv
standalones/SerotypeR/reference/35_loci_mutations.csv
standalones/SerotypeR/reference/41_loci.csv
standalones/SerotypeR/reference/41_loci_lookup.csv
standalones/SerotypeR/reference/GBS_loci.csv
standalones/SerotypeR/reference/GBS_loci_lookup.csv
standalones/SerotypeR/reference/GBS_loci_mutations.csv
standalones/SerotypeR/reference/Lookups_All_Serogroups.xlsx
standalones/SerotypeR/reference/blast_evalues.csv
standalones/SerotypeR/wildgenes/06_wciN_1.fasta
standalones/SerotypeR/wildgenes/06_wciN_2.fasta
standalones/SerotypeR/wildgenes/06_wciN_3.fasta
standalones/SerotypeR/wildgenes/06_wciP.fasta
standalones/SerotypeR/wildgenes/06_wzy.fasta
standalones/SerotypeR/wildgenes/07_wcwD.fasta
standalones/SerotypeR/wildgenes/07_wcwK.fasta
standalones/SerotypeR/wildgenes/09_wchA.fasta
standalones/SerotypeR/wildgenes/09_wcjA.fasta
standalones/SerotypeR/wildgenes/09_wcjB.fasta
standalones/SerotypeR/wildgenes/09_wcjD.fasta
standalones/SerotypeR/wildgenes/09_wcjE.fasta
standalones/SerotypeR/wildgenes/09_wzy.fasta
standalones/SerotypeR/wildgenes/10_wcrC_10A.fasta
standalones/SerotypeR/wildgenes/10_wcrC_10B.fasta
standalones/SerotypeR/wildgenes/11_gct.fasta
standalones/SerotypeR/wildgenes/11_wcjE.fasta
standalones/SerotypeR/wildgenes/11_wcrL.fasta
standalones/SerotypeR/wildgenes/11_wcwC.fasta
standalones/SerotypeR/wildgenes/11_wcwR.fasta
standalones/SerotypeR/wildgenes/12_wciI.fasta
standalones/SerotypeR/wildgenes/12_wcxD.fasta
standalones/SerotypeR/wildgenes/12_wcxF.fasta
standalones/SerotypeR/wildgenes/12_wzy.fasta
standalones/SerotypeR/wildgenes/15_glf.fasta
standalones/SerotypeR/wildgenes/15_rmlB.fasta
standalones/SerotypeR/wildgenes/15_rmlD.fasta
standalones/SerotypeR/wildgenes/15_wchL.fasta
standalones/SerotypeR/wildgenes/15_wciZ.fasta
standalones/SerotypeR/wildgenes/15_wcjE.fasta
standalones/SerotypeR/wildgenes/15_wzd.fasta
standalones/SerotypeR/wildgenes/18_glf.fasta
standalones/SerotypeR/wildgenes/18_wciX.fasta
standalones/SerotypeR/wildgenes/18_wcxM.fasta
standalones/SerotypeR/wildgenes/19_HG264.fasta
standalones/SerotypeR/wildgenes/19_glf.fasta
standalones/SerotypeR/wildgenes/19_wchU.fasta
standalones/SerotypeR/wildgenes/22_wcwA.fasta
standalones/SerotypeR/wildgenes/22_wcwC.fasta
standalones/SerotypeR/wildgenes/23_wchA.fasta
standalones/SerotypeR/wildgenes/23_wchA_23A.fasta
standalones/SerotypeR/wildgenes/23_wchA_23BF.fasta
standalones/SerotypeR/wildgenes/23_wzy_23A.fasta
standalones/SerotypeR/wildgenes/23_wzy_23A_delete.fasta
standalones/SerotypeR/wildgenes/23_wzy_23B.fasta
standalones/SerotypeR/wildgenes/23_wzy_23BF_delete.fasta
standalones/SerotypeR/wildgenes/23_wzy_23F.fasta
standalones/SerotypeR/wildgenes/24_glf.fasta
standalones/SerotypeR/wildgenes/24_wzy.fasta
standalones/SerotypeR/wildgenes/25_wcyC.fasta
standalones/SerotypeR/wildgenes/25_wcyD.fasta
standalones/SerotypeR/wildgenes/25_wcyV.fasta
standalones/SerotypeR/wildgenes/28_wciU.fasta
standalones/SerotypeR/wildgenes/32_HG271.fasta
standalones/SerotypeR/wildgenes/33_tts.fasta
standalones/SerotypeR/wildgenes/33_wciB.fasta
standalones/SerotypeR/wildgenes/33_wciN_33B.fasta
standalones/SerotypeR/wildgenes/33_wciN_33D.fasta
standalones/SerotypeR/wildgenes/33_wcjE.fasta
standalones/SerotypeR/wildgenes/33_wcjE_2.fasta
standalones/SerotypeR/wildgenes/33_wcjE_33A.fasta
standalones/SerotypeR/wildgenes/33_wcjE_33AF.fasta
standalones/SerotypeR/wildgenes/33_wcyO.fasta
standalones/SerotypeR/wildgenes/35_mnp1.fasta
standalones/SerotypeR/wildgenes/35_wciG.fasta
standalones/SerotypeR/wildgenes/35_wcrI.fasta
standalones/SerotypeR/wildgenes/35_wcrK.fasta
standalones/SerotypeR/wildgenes/35_wzh.fasta
standalones/SerotypeR/wildgenes/41_wcrX.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE2.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE3.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE5.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE8.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE_old.fasta
standalones/SerotypeR/wildgenes/GBS_cpsE_short.fasta
standalones/SerotypeR/wildgenes/GBS_cpsF.fasta
standalones/SerotypeR/wildgenes/GBS_cpsG.fasta
standalones/SerotypeR/wildgenes/GBS_cpsH.fasta
standalones/SerotypeR/wildgenes/GBS_cpsH1a.fasta
standalones/SerotypeR/wildgenes/GBS_cpsH1b.fasta
standalones/SerotypeR/wildgenes/GBS_cpsH3.fasta
standalones/SerotypeR/wildgenes/GBS_cpsH8.fasta
standalones/SerotypeR/wildgenes/GBS_cpsI.fasta
standalones/SerotypeR/wildgenes/GBS_cpsI6.fasta
standalones/SerotypeR/wildgenes/GBS_cpsJ.fasta
standalones/SerotypeR/wildgenes/GBS_cpsJ1a.fasta
standalones/SerotypeR/wildgenes/GBS_cpsJ1b.fasta
standalones/SerotypeR/wildgenes/GBS_cpsK.fasta
standalones/SerotypeR/wildgenes/GBS_cpsK1a.fasta
standalones/SerotypeR/wildgenes/GBS_cpsM.fasta
standalones/SerotypeR/wildgenes/GBS_cpsM7.fasta
standalones/SerotypeR/wildgenes/GBS_cpsM_old.fasta
standalones/SerotypeR/wildgenes/GBS_cpsN.fasta
standalones/SerotypeR/wildgenes/GBS_cpsO.fasta
standalones/SerotypeR/wildgenes/GBS_cpsP.fasta
standalones/SerotypeR/wildgenes/GBS_cpsQ.fasta
standalones/SerotypeR/wildgenes/GBS_cpsR.fasta
standalones/WamR-Pneumo/WamR-Pneumo.R
standalones/WamR-Pneumo/WamR-Pneumo_Readme.md
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/ermB.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/folA.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/folP.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/gyrA.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/parC.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/pbp1a.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/pbp2b.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.ndb
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.nhr
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.nin
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.not
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.nsq
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.ntf
standalones/WamR-Pneumo/allele_lkup_dna/pbp2x.fasta.nto
standalones/WamR-Pneumo/allele_lkup_dna/rpsJ.fasta
standalones/WamR-Pneumo/reference/blast_evalues.csv
standalones/WamR-Pneumo/reference/ery_mic_lookup.csv
standalones/WamR-Pneumo/reference/inc_mic_azithromycin.csv
standalones/WamR-Pneumo/reference/inc_mic_ceftriaxone.csv
standalones/WamR-Pneumo/reference/inc_mic_ceftriaxone_nonmen.csv
standalones/WamR-Pneumo/reference/inc_mic_cefuroxime.csv
standalones/WamR-Pneumo/reference/inc_mic_cefuroxime_oral.csv
standalones/WamR-Pneumo/reference/inc_mic_chloramphenicol.csv
standalones/WamR-Pneumo/reference/inc_mic_clarithromycin.csv
standalones/WamR-Pneumo/reference/inc_mic_clindamycin.csv
standalones/WamR-Pneumo/reference/inc_mic_doxycycline.csv
standalones/WamR-Pneumo/reference/inc_mic_erythromycin.csv
standalones/WamR-Pneumo/reference/inc_mic_levofloxacin.csv
standalones/WamR-Pneumo/reference/inc_mic_moxifloxacin.csv
standalones/WamR-Pneumo/reference/inc_mic_penicillin.csv
standalones/WamR-Pneumo/reference/inc_mic_tetracycline.csv
standalones/WamR-Pneumo/reference/inc_mic_trimeth_sulfa.csv
standalones/WamR-Pneumo/reference/loci.csv
standalones/WamR-Pneumo/reference/loci_mutations.csv
standalones/WamR-Pneumo/wildgenes/23S_R6.fasta
standalones/WamR-Pneumo/wildgenes/ARG-ANNOT database.fasta
standalones/WamR-Pneumo/wildgenes/NCCP11945_23S4.fasta
standalones/WamR-Pneumo/wildgenes/PBP1A_TIGR4.fasta
standalones/WamR-Pneumo/wildgenes/PBP1A_Taiwan19F_14.fasta
standalones/WamR-Pneumo/wildgenes/PBP2B_R6_2.fasta
standalones/WamR-Pneumo/wildgenes/PBP2B_Taiwan19F_14.fasta
standalones/WamR-Pneumo/wildgenes/PBP2X_Taiwan19F_14.fasta
standalones/WamR-Pneumo/wildgenes/cat.fasta
standalones/WamR-Pneumo/wildgenes/ermB.fasta
standalones/WamR-Pneumo/wildgenes/ermTR.fasta
standalones/WamR-Pneumo/wildgenes/folA.fasta
standalones/WamR-Pneumo/wildgenes/folP.fasta
standalones/WamR-Pneumo/wildgenes/gyrA.fasta
standalones/WamR-Pneumo/wildgenes/mefAE.fasta
standalones/WamR-Pneumo/wildgenes/mefE.fasta
standalones/WamR-Pneumo/wildgenes/mega_element.fasta
standalones/WamR-Pneumo/wildgenes/parC.fasta
standalones/WamR-Pneumo/wildgenes/pbp1a.fasta
standalones/WamR-Pneumo/wildgenes/pbp2b.fasta
standalones/WamR-Pneumo/wildgenes/pbp2x.fasta
standalones/WamR-Pneumo/wildgenes/rpsJ.fasta
standalones/WamR-Pneumo/wildgenes/tetM.fasta
standalones/WamR-Pneumo/wildgenes/tetO.fasta
standalones/WamR-Pneumo/wildgenes/tetO_GAS.fasta
