sra-data-retrieval-pipelines

This repository contains a collection of bioinformatics workflows for retrieving and processing biological data from NCBI databases using multiple programming approaches.

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Project overview

The aim of this project is to demonstrate reproducible data retrieval and transformation workflows using:

• R
• Python
• Bash

These workflows cover both single accession retrieval and batch data processing from the Sequence Read Archive (SRA).

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Repository structure

Each branch represents a specific workflow:

1. r-single-accession

• Retrieve a single GenBank accession using R
• Outputs:
  • FASTA
  • GenBank (.gb)
  • Metadata (.csv)
  • Full metadata (.json)

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2. r-multiple-sra

• Download multiple SRA accessions using R
• Automates batch retrieval of FASTQ files

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3. python-multiple-sra

• Python-based workflow for downloading multiple SRA datasets

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4. bash-multiple-sra

• Command-line (Bash) workflow using SRA Toolkit

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Technologies used

• R (rentrez, xml2, jsonlite, tidyverse)
• Python
• Bash (SRA Toolkit)
• Git & GitHub for version control

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Key skills

• Programmatic access to NCBI databases
• Handling multiple bioinformatics file formats
• Batch processing using loops
• Reproducible workflows using RMarkdown
• Structured project organization using Git branches

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Getting started

Clone the repository:

git clone https://github.com/N-mogoi/biological_databases_ontology.git
cd biological_databases_ontology

Switch to a branch of interest:

git checkout r-single-accession

Author

Nick Mogoi Bioinformatics | R | Python | Genomics

Connect GitHub: https://github.com/N-mogoi LinkedIn: www.linkedin.com/in/nick-mogoi-2023b2173