Alternatives and similar repositories for BTyper3:

Users that are interested in BTyper3 are comparing it to the libraries listed below

• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 2 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated this week
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆21Updated 2 weeks ago
• cruizperez / FastAAI
  ☆11Updated 2 months ago
• jonas-fuchs / virHEAT
  Visualize microbial evolution at the SNP level!
  ☆14Updated 5 months ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 2 months ago
• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆27Updated this week
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆34Updated 3 weeks ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆29Updated 2 weeks ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated last week
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated last week
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated last week
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• katholt / AMRrules
  Organism-specific interpretation of AMR genotypes
  ☆10Updated 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 11 months ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• oschwengers / tadrep
  Targeted Detection and Reconstruction of Plasmids
  ☆20Updated 11 months ago
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated 10 months ago
• lmc297 / bactaxR
  Bacterial taxonomy construction and evaluation in R
  ☆13Updated last year
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆36Updated last month
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 6 years ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 6 months ago
• rpetit3 / assembly-scan
  Generate basic stats for an assembly.
  ☆11Updated 2 years ago
• lgpdevtools / sraX
  Systematic resistome analysis
  ☆10Updated 5 years ago
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 2 years ago