nickjcroucher / gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
☆182Updated 2 weeks ago
Alternatives and similar repositories for gubbins:
Users that are interested in gubbins are comparing it to the libraries listed below
- BSR-Based Allele Calling Algorithm☆141Updated 2 weeks ago
- snipit: summarise snps relative to your reference sequence☆155Updated last month
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆140Updated 5 months ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆121Updated last week
- An updated pipeline for pangenome investigation☆288Updated 3 weeks ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆114Updated 10 months ago
- "Reads to report" for public health and clinical microbiology☆139Updated last year
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆113Updated 3 weeks ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆219Updated 2 years ago
- Massively parallel phylogenetic placement of genetic sequences☆82Updated 2 years ago
- Metagenomic classification of long-read sequencing data☆77Updated last week
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆120Updated last year
- MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes☆121Updated 4 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆132Updated last year
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆215Updated last week
- Pan-genome wide association studies☆191Updated 9 months ago
- Making whole bacterial genome sequencing data analysis easy☆103Updated 4 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆108Updated last week
- SKESA assembler☆115Updated 5 months ago
- Foreign Contamination Screening caller scripts and documentation☆129Updated last week
- ☆199Updated 2 months ago
- Benchmarking of long-read assembly tools for bacterial whole genomes☆170Updated 4 years ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆199Updated this week
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆115Updated last year
- The ARTIC field bioinformatics pipeline☆120Updated 2 weeks ago
- fast phage annotation program☆158Updated 2 months ago
- Scan contig files against PubMLST typing schemes☆220Updated 2 years ago
- Processing pipeline for pan-genome visulization and exploration☆138Updated last year
- HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.☆132Updated last year
- A tool for generating consensus long-read assemblies for bacterial genomes☆317Updated 9 months ago