yatisht / usherLinks
Ultrafast Sample Placement on Existing Trees
☆139Updated this week
Alternatives and similar repositories for usher
Users that are interested in usher are comparing it to the libraries listed below
Sorting:
- Depth-weighted De-Mixing☆127Updated this week
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Updated 2 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆119Updated last year
- ☆50Updated 3 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆151Updated 3 weeks ago
- Massively parallel phylogenetic placement of genetic sequences☆86Updated 3 years ago
- Process consensus file for COG-UK data☆14Updated 4 years ago
- Global phylogenies of SARS-CoV-2 sequences☆85Updated 2 years ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆129Updated last year
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Updated 2 weeks ago
- Antibiotic resistance prediction in minutes☆112Updated last year
- Bioinformatics Pipeline and Visualization resources☆60Updated last year
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆119Updated last week
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Updated last year
- Primer schemes for real-time genome epidemiology☆30Updated 2 years ago
- snipit: summarise snps relative to your reference sequence☆166Updated 2 weeks ago
- A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curat…☆63Updated 4 months ago
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Updated 2 years ago
- The ARTIC fieldbioinformatics pipeline☆128Updated 2 weeks ago
- Making whole bacterial genome sequencing data analysis easy☆114Updated 9 months ago
- Programmatically interact with the GISAID database.☆80Updated 5 months ago
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies☆146Updated last month
- A toolbox for pangenome analysis and threshold evaluation.☆100Updated 3 years ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Updated 11 months ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆132Updated last week
- SEER, reimplemented in python 🐍🔮☆128Updated 8 months ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆148Updated 3 months ago
- WtP: Phage identification via nextflow and docker or singularity☆103Updated this week
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆93Updated last month
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated 2 years ago