genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.
☆168Mar 12, 2026Updated 2 weeks ago
Alternatives and similar repositories for genome_updater
Users that are interested in genome_updater are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆104Mar 21, 2026Updated last week
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆48Feb 5, 2026Updated last month
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆298Feb 3, 2026Updated last month
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆241Oct 12, 2025Updated 5 months ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆208Sep 22, 2023Updated 2 years ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- Recombination-free trees☆63Sep 1, 2025Updated 6 months ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆137Mar 19, 2026Updated last week
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- Approximate nearest neighbour search for microbial genomes based on hash metric☆62Mar 7, 2026Updated 3 weeks ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated 2 months ago
- A repo with just adapter sequences☆15Jul 7, 2025Updated 8 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆613Feb 18, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆82Mar 12, 2026Updated 2 weeks ago
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated 8 months ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 4 months ago
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆217Mar 13, 2026Updated 2 weeks ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆53Updated this week
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- ☆84Sep 13, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Logan Unitigs and Contigs☆185Sep 14, 2025Updated 6 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆49Mar 2, 2026Updated 3 weeks ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Mar 21, 2026Updated last week
- A genomic minhashing implementation in Rust☆103Jun 17, 2025Updated 9 months ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆75Mar 14, 2026Updated 2 weeks ago
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆43Apr 8, 2024Updated last year
- Strain resolver for metagenomics☆80Aug 2, 2024Updated last year
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Mar 16, 2026Updated last week
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆175Feb 26, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Remove human reads from a sequencing run☆48Mar 9, 2026Updated 2 weeks ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Simple Python interface to CoverM's fast coverage estimation functions☆10Dec 20, 2024Updated last year
- Reorients assembled microbial sequences☆136Aug 21, 2025Updated 7 months ago
- Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes☆184Updated this week
- Read alignment statistics for metagenomics☆395Mar 16, 2026Updated last week
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆179Mar 17, 2026Updated last week