Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Rapid determination of appropriate reference genomes.

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

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.

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

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

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

Pipeline for the selection of canonical proteins for reference proteomes

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

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

Mapping RefSeq RNA to OrthoDB (Under Development)

NCBI Genome downloader

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

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

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

Downloading Genomes from RefSeq

Randomly download genomes from NCBI RefSeq and Genbank

🦇🧫📊Supplementary materials for study on bat gut shotgun metagenomics