GenEpiO / genepioLinks
The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
☆21Updated this week
Alternatives and similar repositories for genepio
Users that are interested in genepio are comparing it to the libraries listed below
Sorting:
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆14Updated last month
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆43Updated last month
- Bacterial Annotation by Learned Representation of Genes☆58Updated 4 years ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 6 months ago
- Python bindings for the TaxonKit library☆40Updated 3 months ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)☆48Updated 9 months ago
- ☆31Updated 3 years ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆25Updated 2 months ago
- ☆26Updated 3 months ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Updated 4 years ago
- ☆41Updated 4 months ago
- Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data☆59Updated last year
- Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!☆27Updated last month
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆75Updated 3 months ago
- Detection of incorrectly labeled sequences across kingdoms☆85Updated 2 years ago
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆64Updated last week
- ☆16Updated last year
- Influenza genome analysis Nextflow workflow☆28Updated 3 weeks ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated 9 months ago
- A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers☆50Updated 8 months ago
- fast sequence evolution simulation for SARS-CoV-2 and similar☆22Updated 6 months ago
- A selection of short scripts for analyzing microbial genomes☆14Updated 7 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated last month
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 3 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- a python package for automated generation of phylogenetic trees from genbank files☆23Updated 7 months ago
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Updated 3 months ago
- sunburst plots for taxonomy - working to update Krona☆40Updated 2 weeks ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆29Updated last month