🧬 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.
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.
Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.
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
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
VAPiD: Viral Annotation and Identification Pipeline
A Python package for obtaining, parsing and exploring 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
Get citation counts for a PubMed paper from the command line
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