jessiewu / bacterialGWASLinks
A pipeline for performing genome-wide association tests for bacterial genomes.
☆27Updated 7 years ago
Alternatives and similar repositories for bacterialGWAS
Users that are interested in bacterialGWAS are comparing it to the libraries listed below
Sorting:
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 3 years ago
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆21Updated 8 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Locus and lineage tests for bacterial GWAS☆29Updated 8 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 4 years ago
- Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.☆19Updated 7 years ago
- A set of scripts for calculating pairwise SNP distance☆43Updated 2 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆15Updated 3 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- ☆37Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Strain Prediction and Analysis with Representative SEquence☆19Updated last year
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆22Updated last year
- genomic alignment similarity search tool☆18Updated 7 months ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆63Updated 5 years ago
- Gene-flank analysis tool☆34Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆33Updated 2 years ago
- Tools for extracting individual genomes from metagenomes☆16Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …☆47Updated 3 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆39Updated 3 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 5 years ago
- ☆26Updated 4 years ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆33Updated 3 years ago