| buildSNVtable | M1UK typing pipeline from WGS SNVPhyl M1UK Analysis July 3,... |
| EMM_pipeline | emm typing pipeline from WGS assemblies February 5 2024,... |
| find_sample_duplicates | Duplicate Samples Finder February 5 2024, Walter Demczuk &... |
| getdirectory | Common helper functions for WADE analysis July 3, 2024,... |
| labware_gas_amr | Labware Upload Formatter for GAS AMR July 3, 2024, Walter... |
| labware_gas_toxins | Labware Upload Formatter for GAS Toxins February 5 2024,... |
| labware_gbs_amr | Labware Upload Formatter for GBS AMR February 5 2024, Walter... |
| labware_gono_amr | Labware Upload Formatter for GONO AMR July 3 2024, Walter... |
| labware_pneumo_amr | Labware Upload Formatter for PNEUMO AMR July 3 2024, Walter... |
| labware_pneumo_virulence | Labware Upload Formatter for PNEUMO VIRULENCE February 5... |
| MakeblastDB_pipeline | Makeblastdb.R indexes Blast fasta databases July 3, 2024,... |
| MASTER_pipeline | Molecular typing pipeline for WGS assemblies July 3 2024,... |
| metrics | Labware Upload Formatter for WGS Metrics February 5 2024,... |
| MIC_compare | Detects potententially contaminated samples based on plate... |
| MLST_pipeline | MLST pipeline for WGS assemblies July 3, 2024, Walter Demczuk... |
| nwk_sort_order | Gets the sort order for samples from a newick tree file.... |
| proximity_test | Detects potententially contaminated samples based on plate... |
| remove_duplicates_fasta | Fasta Duplicates Remover February 5 2024, Shelley Peterson... |
| rename_fastqs | Renames submitted WGS reads to NML LabWare numbers July 3,... |
| rename_submitted | Renames submitted contig files to NML LabWare numbers... |
| rRNA16S_pipeline | 16SrRNA Pipeline February 5 2024, Walter Demczuk & Shelley... |
| rRNA23S_pipeline | 23S rRNA pipeline for WGS assemblies to determine number of... |
| SEROTYPE_pipeline | Serotyping pipeline for WGS assemblies February 5 2024,... |
| update_lookups | July 3, 2024, Shelley Peterson |
