Alternatives and similar repositories for meningotype

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

• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆15Updated 2 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 8 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 3 months ago
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated 2 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated this week
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated this week
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆19Updated 2 years ago
• combogenomics / CONTIGuator
  Bacterial genomes finishing tool for structural insights on draft genomes
  ☆23Updated 2 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 2 years ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆27Updated 3 years ago
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆27Updated 3 weeks ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆25Updated 3 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆29Updated 3 months ago
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆43Updated 2 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆64Updated 4 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆31Updated 6 months ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated this week
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• FOI-Bioinformatics / nanometa_live
  A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…
  ☆18Updated last year
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 2 years ago
• ukhsa-collaboration / PneumoCaT
  Pneumococcal Capsular Typing tool for NGS data
  ☆18Updated 4 years ago