Alternatives and similar repositories for emmtyper

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

• DOH-JDJ0303 / bigbacter-nf
  Bacterial surveillance pipeline.
  ☆24Updated last month
• UPHL-BioNGS / Donut_Falls
  Assembly of Nanopore Sequencing
  ☆16Updated last month
• nickp60 / EzClermont
  Phylotype your strains using Clermont's 2013 method: ezclermont.org
  ☆11Updated 2 years ago
• appliedbinf / el_gato
  ☆10Updated 3 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last month
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated 2 weeks ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• Public-Health-Bioinformatics / pubmlst_client
  List and download schemes from pubMLST.org and other BIGSDB servers
  ☆10Updated 9 months ago
• microbinfie-hackathon2020 / CSIS
  Code Safety Inspection Service
  ☆20Updated 2 years ago
• labgem / PlaScope
  Plasmid exploration of bacterial genomes
  ☆18Updated 3 years ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• scwatts / hicap
  in silico typing of the H. influenzae cap locus
  ☆12Updated last year
• mbhall88 / ontime
  Extract subsets of ONT (Nanopore) reads based on time
  ☆22Updated 10 months ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆36Updated 4 months ago
• lskatz / lyve-SET
  LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
  ☆27Updated 10 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated 2 years ago
• Ivarz / Conifer
  Calculate confidence scores from Kraken2 output
  ☆22Updated last year
• iqbal-lab-org / viridian
  ☆21Updated 4 months ago
• phac-nml / mikrokondo
  A simple pipeline for bacterial assembly and quality control
  ☆17Updated this week
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• staphopia / staphopia-sccmec
  Archived - please see updated sccmec tool at link below
  ☆13Updated 10 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 3 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• phac-nml / rebar
  REcombination BARcode detector.
  ☆16Updated last year
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆32Updated 2 months ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆28Updated last week
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 9 months ago
• lskatz / fundamentals-of-bioinformatics
  ☆26Updated last month
• epi2me-labs / wf-flu
  ☆16Updated last month
• jmcbroome / BTE
  Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit
  ☆14Updated last month