| buildSNVtable | M1UK typing pipeline from WGS SNVPhyl M1UK Analysis December... |
| EMM_pipeline | emm typing pipeline from WGS assemblies December 21 2023,... |
| find_sample_duplicates | Duplicate Samples Finder December 21 2023, Walter Demczuk &... |
| getdirectory | Common helper functions for WADE analysis December 21 2023,... |
| labware_gas_amr | Labware Upload Formatter for GAS AMR December 21 2023, Walter... |
| labware_gas_toxins | Labware Upload Formatter for GAS Toxins December 21 2023,... |
| labware_gbs_amr | Labware Upload Formatter for GBS AMR December 21 2023, Walter... |
| labware_gono_amr | Labware Upload Formatter for GONO AMR December 21 2023,... |
| labware_pneumo_amr | Labware Upload Formatter for PNEUMO AMR December 21 2023,... |
| labware_pneumo_virulence | Labware Upload Formatter for PNEUMO VIRULENCE December 21... |
| MakeblastDB_pipeline | Makeblastdb.R indexes Blast fasta databases December 21 2023,... |
| MASTER_pipeline | Molecular typing pipeline for WGS assemblies December 21... |
| metrics | Labware Upload Formatter for WGS Metrics December 21 2023,... |
| MIC_compare | Detects potententially contaminated samples based on plate... |
| MLST_pipeline | MLST pipeline for WGS assemblies December 21 2023, Walter... |
| nwk_rename_samples | Replace sequencing sample numbers in a newick tree file... |
| nwk_sort_order | Gets the sort order for samples from a newick tree file.... |
| Org_id | VFDB.R Generic Virulence Factor Profiler :... |
| proximity_test | Detects potententially contaminated samples based on plate... |
| remove_duplicates_fasta | Fasta Duplicates Remover December 21 2023, Shelley Peterson... |
| rename_contigs | Rename Assemblies and move to main contigs folder December 21... |
| rename_submitted | Renames submitted contig files to NML LabWare numbers... |
| rRNA16S_pipeline | 16SrRNA Pipeline December 21 2023, Walter Demczuk & Shelley... |
| rRNA23S_pipeline | 23S rRNA pipeline for WGS assemblies to determine number of... |
| SEROTYPE_pipeline | Serotyping pipeline for WGS assemblies December 21 2023,... |
| update_lookups | December 21 2023, Shelley Peterson |
