Alternatives and similar repositories for bugwas

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

• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆18Updated 9 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
• hzi-bifo / Haploflow
  ☆31Updated last year
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 5 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• will-rowe / groot
  A resistome profiler for Graphing Resistance Out Of meTagenomes
  ☆66Updated 5 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆28Updated 7 months ago
• Gardner-BinfLab / deltaBS
  Quantifying the significance of genetic variation using probabilistic profile-based methods.
  ☆19Updated 4 years ago
• shahab-sarmashghi / Skmer
  Fast and accurate tool for estimating genomic distances between genome-skims
  ☆45Updated last year
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆61Updated 5 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• marbl / harvest
  ☆53Updated 4 years ago
• dayzerodx / counterr
  ☆31Updated last year
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 4 months ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• bcthomas / pullseq
  Utility program for extracting sequences from a fasta/fastq file
  ☆36Updated 7 months ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 4 years ago
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆42Updated 2 years ago
• katholt / RedDog
  ☆36Updated 3 years ago
• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆48Updated 2 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago