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1. typhoidgenomics/TyphiNETtyphoidgenomics/TyphiNETPublic

   TyphiNET online Salmonella Typhi AMR surveillance dashboard.

   JavaScript 7 2

2. GenoParatyphiGenoParatyphiPublic

   Detect AMR mutations in Salmonella Paratyphi A genomes based on VCF or BAM files (mapped to Paratyphi A AKU_12601 reference genome)

   Python

3. SNV_plotterSNV_plotterPublic

   Plots the distribution of heterozygous and homozygous SNV calls from RedDog output

   R

4. typhoidgenomics/genotyphityphoidgenomics/genotyphiPublic

   Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

   Python 30 12

5. SNV_Stats_GeneratorSNV_Stats_GeneratorPublic

   SNV Quality Stats Generator provides summaries of high and low quality SNV calls from the GHRU mapping pipeline

   R

6. OTUStalkerOTUStalkerPublic

   OTUStalker is a small software tool designed to be compatible with QIIME (v1.8.0). Its purpose is to retrieve data pertinent to a single taxonomic group, from a larger (presumably mixed) data set, …

   Java