ncbi

Scripts to download genomes from the NCBI FTP servers

genes and genomes at your fingertips

🐞 Convert NCBI taxonomy dump into lineages

dbSNP

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

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

VAPiD: Viral Annotation and Identification Pipeline

🐣 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

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

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

PLSDB pipeline to collect bacterial plasmids from NCBI

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

PipeTaxon exposes the ncbi taxonomy database as a REST API.

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter

Turbocharge a PubMed literature search using citation counts and data from the NIH

Mapping NCBI Genbank accession to GTDB accession