/sra-annotator

A command-line tool for retrieving annotations from the NCBI SRA.

Primary LanguagePythonMIT LicenseMIT

About

DOI

A command-line tool for retrieving annotations from the NCBI SRA database.

It uses NCBI's Entrez Programming Utilities under the hood to query and retrieve Run-level and Sample-level annotation from the SRA database. Learn more about E-Utilities here: https://www.ncbi.nlm.nih.gov/books/NBK25499/

Installation:

pip install -r requirements.txt

Quick start:

sra-annotator [-q] [-o OUTPUT] [-m {quick,full}] [-f] [-d DICTIONARY] [-v] [-h] query

  • User must specify a query term or use -q to input a list of SRA accessions. An input file or search keyword is required.

  • arguments shown in [] are optional.

Usage details:

Checkout the Wiki page for details.