Alternatives and similar repositories for gubbins

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

• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated 3 weeks ago
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆162Updated 7 months ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆140Updated this week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆222Updated 2 weeks ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆162Updated 2 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆117Updated last year
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆224Updated last month
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆205Updated last year
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆262Updated this week
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆141Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆242Updated this week
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆265Updated last month
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆145Updated this week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆335Updated 2 months ago
• rrwick / Perfect-bacterial-genome-tutorial
  ☆150Updated last year
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆329Updated 9 months ago
• cmks / DAS_Tool
  DAS Tool
  ☆161Updated last year
• PacificBiosciences / pb-metagenomics-tools
  Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
  ☆196Updated 2 months ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆208Updated last year
• chklovski / CheckM2
  Assessing the quality of metagenome-derived genome bins using machine learning
  ☆237Updated 8 months ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆203Updated last month
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆249Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆121Updated last week
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆151Updated 8 months ago
• katholt / srst2
  Short Read Sequence Typing for Bacterial Pathogens
  ☆142Updated 4 years ago
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆253Updated 3 years ago
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆196Updated 2 months ago
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆171Updated 2 weeks ago
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆130Updated last week
• labgem / PPanGGOLiN
  Build a partitioned pangenome graph from microbial genomes
  ☆287Updated 2 weeks ago