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

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.

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