jessiewu / bacterialGWAS
A pipeline for performing genome-wide association tests for bacterial genomes.
☆28Updated 6 years ago
Related projects ⓘ
Alternatives and complementary repositories for bacterialGWAS
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆19Updated 8 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆19Updated 3 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- Gene-flank analysis tool☆26Updated 6 months ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 5 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 3 years ago
- Locus and lineage tests for bacterial GWAS☆30Updated 7 years ago
- ☆33Updated 2 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆44Updated last year
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆20Updated 7 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆29Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆18Updated 2 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 3 months ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆29Updated 3 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Pipeline for metagenome and metatranscriptome joint assembly☆18Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last month
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆30Updated 2 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆26Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆52Updated last year
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆36Updated 10 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆39Updated 4 years ago
- A toolkit for prokaryotic comparative genomics☆25Updated 2 months ago
- Assembly by Reduced Complexity (ARC)☆41Updated 8 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆18Updated 5 years ago