Ncbi Python Packages

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

gget

🧬 gget enables efficient querying of genomic reference databases

genomepy

genes and genomes at your fingertips

pubmed-search-mcp

🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

pypubmed

Toolkits for NCBI Pubmed

pmidcite

Turbocharge a PubMed literature search using citation data from the NIH

http-stream-xml

Parse HTTP response as stream, by chunks. Example for NCBI (PubMed) Entrez.

clinvar-this

ClinVar Submission API Made Easy

multitax

Python package to obtain, parse and explore biological and custom taxonomies.

taxadb

:hatching_chick: locally query the ncbi taxonomy

medirect

Multithreaded ncbi edirect and ftract

pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

pubmed2

search pubmeds quickly

elastic-blast

ElasticBLAST runs BLAST searches faster by distributing its work to multiple cloud instances. This allows larger numbers of queries to be searched in less time compared to BLAST+ on a single host. Use of the cloud facilitates collaboration, sharing of results, datasets and pipelines on a common platform. The National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov)), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.

taxidtools

Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files

ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

pyncbi

A Python API library for exploration and data retrieval from NCBI

ncbi-submit

A tool for submitting to NCBI (SRA, BioSample, & GenBank).

taxonomy-ranks

To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)

genome-collector

Easily download and store taxID genomes from NCBI

datasnakes

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

enigmadatabase

NCBI DNA Database Builder and Dataset Loader for ML pipelines (Enigma2).

bioinformatics-mcp-server

MCP server for bioinformatics data — genes, proteins, PubMed, ClinVar and sequences via NCBI & UniProt (free, no API key)