Alternatives and similar repositories for pGWAS

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

• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆27Updated 3 years ago
• kwongj / contig-puller
  Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence
  ☆13Updated 7 years ago
• GDKO / AvP
  Automatic evaluation of HGTs
  ☆30Updated last year
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 5 years ago
• cjneely10 / EukMetaSanity
  Structural and functional annotation of eukaryotic metagenome-assembled genomes
  ☆22Updated 2 years ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• BenoitMorel / AleRax
  Gene tree - species tree reconciliation from gene tree distributions
  ☆40Updated 2 months ago
• tseemann / scapper
  Whole genome core alignments from multiple draft genomes
  ☆13Updated 9 years ago
• ThomasArn / genoPlotR_wrapper
  Wrapper for the genoPlotR R package. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR p…
  ☆14Updated 4 years ago
• laxeye / zga
  ZGA prokaryotic genome assembly and annotation pipeline
  ☆13Updated last year
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆35Updated 2 years ago
• Shamir-Lab / SCAPP
  SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…
  ☆36Updated 2 years ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆27Updated 10 months ago
• wandreopoulos / deeplasmid
  ☆20Updated last year
• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆35Updated 7 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆63Updated 2 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆65Updated 7 months ago
• vinuesa / get_phylomarkers
  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…
  ☆60Updated 2 months ago
• PlantDr430 / FunFinder_Pangenome
  Data analysis of Funannotate and Orthofinder outputs to Pangenome results
  ☆23Updated 5 years ago
• Sudaraka88 / LDWeaver
  Genomewide Epistasis Analysis on Bacteria
  ☆15Updated 8 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆46Updated this week
• alexcritschristoph / soil_popgen
  Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes
  ☆16Updated 5 years ago
• ukhsa-collaboration / LOMA
  A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
  ☆17Updated 10 months ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆50Updated last year
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 9 months ago
• bcgsc / ntSynt-viz
  Multi-genome synteny block visualization tool
  ☆52Updated last week
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated 3 weeks ago
• bvalot / panISa
  panISa is a software to search insertion sequence (IS) on resequencing data (bam file)
  ☆24Updated last year
• chmccarthy / Pangloss
  Pangenome analysis of eukaryotes.
  ☆21Updated 5 years ago