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.
☆23Updated 3 months ago
Alternatives and similar repositories for genepio
Users that are interested in genepio are comparing it to the libraries listed below
Sorting:
- Bacterial Annotation by Learned Representation of Genes☆58Updated 4 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- ☆31Updated 4 years ago
- A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers☆52Updated last month
- ☆52Updated 8 months ago
- Python bindings for the TaxonKit library☆41Updated last month
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- fast sequence evolution simulation for SARS-CoV-2 and similar☆22Updated 8 months ago
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆47Updated 2 weeks ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆45Updated 2 weeks ago
- Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!☆27Updated last month
- Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)☆51Updated last year
- ☆26Updated 6 months ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆14Updated 4 months ago
- Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes☆28Updated last year
- Influenza genome analysis Nextflow workflow☆31Updated 3 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆44Updated 9 months ago
- MGnify API toolkit☆19Updated 11 months ago
- A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.☆28Updated last week
- SMBGC Annotation using Neural Networks Trained on Interpro Signatures☆29Updated 8 months ago
- Reference-guided multiple sequence alignment of viral genomes☆70Updated 2 months ago
- Detection of incorrectly labeled sequences across kingdoms☆87Updated 3 years ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆82Updated last month
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Updated 3 years ago
- Nail is an Alignment Inference tooL☆54Updated this week
- codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the…☆13Updated last month
- Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).☆50Updated 3 years ago
- Pipeline to apply encoded Kmer analysis to protein sequences☆16Updated 3 weeks ago
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Updated last month
- Fast and space-efficient taxonomic classification of long reads☆42Updated 4 months ago