Alternatives and similar repositories for pairsnp

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

• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• sanger-pathogens / plasmidtron
  Assembling the cause of phenotypes and genotypes from NGS data
  ☆29Updated 5 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 10 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆67Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 2 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 5 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated last month
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• katiesaund / hogwash
  Three bacterial GWAS methods all rolled into one easy-to-use R package
  ☆22Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆53Updated 2 weeks ago
• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆48Updated 2 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• katholt / RedDog
  ☆37Updated 3 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 8 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆64Updated 4 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 3 months ago
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆32Updated 3 years ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 7 months ago
• harry-thorpe / piggy
  Pipeline for analysing intergenic regions in bacteria
  ☆40Updated 6 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago