sanger-pathogens / BaGPipeLinks
A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge
☆21Updated last week
Alternatives and similar repositories for BaGPipe
Users that are interested in BaGPipe are comparing it to the libraries listed below
Sorting:
- Bacterial GWAS analysis☆46Updated 2 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 9 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated last month
- A toolkit for prokaryotic comparative genomics☆51Updated 3 months ago
- IslandPath standalone software☆35Updated 2 years ago
- SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.☆24Updated 2 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Updated last week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 7 months ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- ☆25Updated last year
- Calculate assocations between genes and traits☆29Updated 10 months ago
- Prophage Activity Estimator☆30Updated last year
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆71Updated 3 weeks ago
- Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing☆19Updated last year
- Microbial agile accurate SNP Typer☆30Updated 2 years ago
- ☆34Updated 2 years ago
- Build a map of genes present across a set of microbial genomes☆18Updated last week
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆39Updated 3 years ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆40Updated 3 years ago
- Analysing the genomic context of mobile genes☆11Updated 6 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆34Updated 6 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆18Updated last year
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆15Updated 3 years ago
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆44Updated 2 months ago