Alternatives and similar repositories for AgrVATE

Users that are interested in AgrVATE are comparing it to the libraries listed below

• katholt / AMRrules
  Organism-specific interpretation of AMR genotypes
  ☆14Updated last year
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆15Updated 2 years ago
• shengzheBian / VPsero
  rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes
  ☆10Updated 4 years ago
• klebgenomics / Kleborate-viz
  Visualisation application for Klebsiella genotypes generated by Kleborate.
  ☆10Updated 2 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 4 months ago
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆15Updated 2 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 9 months ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• staphopia / staphopia-sccmec
  Archived - please see updated sccmec tool at link below
  ☆13Updated last year
• CFIA-NCFAD / wgscovplot
  The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…
  ☆19Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆27Updated last month
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 3 years ago
• mdsufz / OrtSuite
  Prediction of microbial interactions in complex communities
  ☆11Updated last year
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆26Updated this week
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆39Updated 9 months ago
• yosuken / ccfind
  ccfind - circular complete genome finder with clues of terminal redundancy
  ☆16Updated 5 years ago
• LanLab / ShigEiFinder
  Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
  ☆12Updated 2 years ago
• appliedbinf / el_gato
  ☆10Updated 7 months ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆13Updated last year
• moritzbuck / mOTUlizer
  Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin
  ☆14Updated last year
• janka2012 / digIS
  Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes
  ☆11Updated 4 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 3 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆31Updated this week
• ukhsa-collaboration / LOMA
  A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
  ☆16Updated 8 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated last year
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆24Updated 2 years ago
• farhat-lab / fast-lineage-caller
  ☆14Updated 4 years ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• DOH-JDJ0303 / bigbacter-nf
  Bacterial surveillance pipeline.
  ☆26Updated last month