Alternatives and similar repositories for RCandy

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

• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆60Updated 2 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆43Updated 2 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆29Updated 8 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆43Updated last month
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆32Updated last month
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆27Updated 4 years ago
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆49Updated last month
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆36Updated 4 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 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
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆26Updated 3 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆61Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆25Updated 5 months ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆31Updated last month
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆33Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 5 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆30Updated 10 months ago
• Sudaraka88 / LDWeaver
  Genomewide Epistasis Analysis on Bacteria
  ☆14Updated 3 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 3 years ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆24Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆46Updated 2 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year