🧬 gget enables efficient querying of genomic reference databases
Scripts to download genomes from the NCBI FTP servers
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
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
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
VAPiD: Viral Annotation and Identification Pipeline
Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
🐣 locally query the ncbi taxonomy
Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
Download "Cited by" data from the NIH for any paper with a PubMed ID
A Model Context Protocol (MCP) server enabling AI agents to intelligently search, retrieve, and analyze biomedical literature from PubMed via NCBI E-utilities. Includes a research agent scaffold. STDIO & HTTP
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