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.

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Rapid determination of appropriate reference genomes.

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Fast and space-efficient taxonomic classification of long reads

F# library for accessing and manipulating bioinformatic datasets.

Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories

fast classification of metagenomic sequences with lightweight de Bruijin graph-based reference indexing

Download biological databas, extract database identifier and entrez gene identifier, insert in a mongo database

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

Pipeline for the selection of canonical proteins for reference proteomes

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

Mapping RefSeq RNA to OrthoDB (Under Development)

Curated mirror of RefSeq Microbial Genomes. Available via CVMFS repository.

🦇🧫📊Study on bat gut shotgun metagenomics

NCBI Genome downloader

Downloading Genomes from RefSeq

Get the latest gene-transcript identifiers using Ensembl, RefSeq, MANE and LRGs models.

⬇️ Facilitates downloading NCBI's RefSeq with a human-readable file structure

🇨🇭🦠 Service for pathogens and threats identification in hospital environments - SOPHiA Genetics