blastdbbuilder 1.0.5

Automated genome download, concatenation, and BLAST database builder

blastdbbuilder: Building a Customised BLASTn Database

M. Asaduzzaman Prodhan^*

DPIRD Diagnostics and Laboratory Services

Department of Primary Industries and Regional Development

3 Baron-Hay Court, South Perth, WA 6151, Australia

*Correspondence: [e-mail]; [e-mail]

Content

• Introduction
• blastdbbuilder
• Features
• Pre-requisite
• Installation
• Usage
  • Step 1. Download Genomes
  • Step 2. Concatenate Genomes
  • Step 3. Build BLAST Database
  • Final Files
• Citation
• Support

Introduction

A BLASTn database provides the essential reference framework for comparing query sequences, forming the backbone of any sequence-based analysis. Accurate results—whether in diagnostics, biosecurity surveillance, microbial studies, evolutionary research, environmental surveys, or functional genomics—depend on a high-quality, well-curated database; without it, even the most sophisticated tools can yield ambiguous outcomes.

Public databases are comprehensive but rapidly expanding, often containing redundant or low-quality and irrelevant entries. This leads to slower searches and reduced search resolution.

In contrast, a custom database is like a well-organised library where every book is precisely indexed— smaller in volume, faster to search, and more focused in results.

However, manually constructing a custom database from numerous genomes is tedious, error-prone, and frequently interrupted by the “Duplicate ID Found” error— with little guidance available on how to resolve it.

To bridge this gap, I developed the blastdbbuilder package — an automated solution for genome download, curation, and database construction. It eliminates common errors, ensures reproducibility, and delivers an optimized, high-quality BLASTn database tailored for diagnostics, biosecurity surveillance, microbial research, and any study that relies on robust sequence comparison.

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blastdbbuilder

blastdbbuilder is a lightweight, command-line toolkit that automates the complete BLASTn database preparation workflow. It streamlines every step — from downloading user-specified genomes and organizing datasets to building optimized, up-to-date BLASTn databases.

Designed for researchers and clinicians, it provides a reproducible, portable, and regularly updated solution for constructing BLASTn databases without manual setup.

The toolkit leverages:

• Singularity containers
• Modular shell scripts

Which enables:

• Easy deployment across diverse computational environments
• No dependency installation
• A smooth and user-friendly experience
• Automatic cleanup of intermediate files, retaining only the final BLASTn database and significantly reducing disk space requirements

Additionally, blastdbbuilder retrieves genomes directly from NCBI’s FTP servers, ensuring that all sequences are as current as the time of download.

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Features

• Automated download of all genomes for virus and the reference genomes for Archaea, Bacteria, Fungi, and Plants

• Resume-able BLASTn database creation — continue from interrupted runs

• Modular bash scripts for each task

• Use of Singularity containers for less software installation and portability

• Lightweight installation

• Less disk space requirement

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Pre-requisite

System requirements

Before installing blastdbbuilder, make sure the following are available on your system:

Python ≥ 3.9

Check your Python version:

python3 --version

If Python is older than 3.9, install a newer Python using your system package manager.

Example (Ubuntu):

sudo apt install python3

This installs the latest Python version supported by your operating system.

You do not need to remove the existing Python installation, because Ubuntu uses Python internally for many system tools.

unzip

The program requires the unzip utility to extract downloaded genome archives.

Check if unzip is installed:

unzip -v

If the command is not found, install it:

sudo apt install unzip

Container engine

One of the following container engines must be installed:

• Apptainer

• SingularityCE ≥ 3.x

Example installation on Ubuntu / Debian:

sudo apt install singularity-container

The program automatically detects which container engine is available on your system and uses it.

On HPC systems (for example ARDC Nectar), Singularity or Apptainer is typically already installed.

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Installation

Install blastdbbuilder directly from PyPI:

pip install blastdbbuilder

Verify installation

Check if the installation was successful:

blastdbbuilder --help

If you see the following usage flags, then

• the installation has been successful

• you can run blastdbbuilder from any directory in your computer

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usage: blastdbbuilder [-h] [--download] [--concat] [--build] [--citation] [--archaea] [--bacteria] [--fungi]
                      [--virus] [--plants]

blastdbbuilder: Automated genome download, concatenation, and BLAST database builder

options:
  -h, --help  show this help message and exit
  --download  Download genomes for selected groups
  --concat    Concatenate all genomes into one FASTA
  --build     Build BLAST database from concatenated FASTA
  --citation  Print citation information
  --archaea   Include Archaea genomes
  --bacteria  Include Bacteria genomes
  --fungi     Include Fungi genomes
  --virus     Include Virus genomes (all)
  --plants    Include Plant genomes

Check the installed version:

blastdbbuilder --version

Upgrade blastdbbuilder

pip install --upgrade blastdbbuilder

Optional: Install from GitHub (development version)

If you want to install the latest development version from GitHub:

git clone https://github.com/AsadProdhan/blastdbbuilder.git
cd blastdbbuilder
pip install -e .

If you want to uninstall blastdbbuilder, run the following command in the same directory where you have installed blastdbbuilder.

pip uninstall blastdbbuilder -y

Check if the uninstallation has been successful

blastdbbuilder --help

Now, you will see an error.

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Usage

• There are three steps from downloading the genomes to building a BLASTn database

• Open a terminal

• Make a directory. Name it based on which group/s you are going to download. For example

  mkdir bacteria
  

• Or, maybe something like this if you are going to download archaea (a), bacteria (b), fungi (f), virus (v), and plants (p). This will help remember what are in the database files which will look like nt.001, nt.002, nt.003 and so on

  mkdir abfvp
  

• Now cd to that directory

  cd abfvp
  

• In this directory, run the following three steps- download, concat and build - sequentially

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Step 1. Download genomes

Download Archaea genomes

blastdbbuilder --download --archaea

This will create an "archaea" directory (db/archaea) and download the archaeal genomes there. Same for the other groups as well

Download Bacteria genomes

blastdbbuilder --download --bacteria

Download Fungal genomes

blastdbbuilder --download --fungi

Download Viral genomes

blastdbbuilder --download --virus

Download Plant genomes

blastdbbuilder --download --plants

Download multiple groups simultaneously in varius combinations of your interest

blastdbbuilder --download --archaea --bacteria 

Or,

blastdbbuilder --download --archaea --bacteria --fungi --virus --plants

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Step 2. Concatenate genomes

After downloading, run the following command.

blastdbbuilder --concat

This will create a directory called concat and put the concatenated file (containing all the downloaded genomes) in there

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Step 3. Build BLAST database

Finally, run the following command.

blastdbbuilder --build

• This will build a BLASTn database from the concatenated FASTA file

• When the run finished, it will clean up all the intermediate files and directories to reduce disk space usage

• You will see only one directory named blastnDB

• blastnDB will contain all the database files, nt.001, nt.002 etc

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Final Files

After running, the directory structure will look like:

blastnDB/
├─ nt.001.fna.gz
├─ nt.002.fna.gz
├─ nt.003.fna.gz
├─ nt.004.fna.gz
├─ nt.nl        
├─ logs/
  ├─ nt.001.log
  ├─ nt.002.log
  ├─ nt.003.log
  └─ nt.004.log

You have just created your customised BLASTn database. It is fully portable, can be moved to other users/computers and used without making any changes

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Citation

Cite this repository

If you use this software in your work, please cite it as follows:

Prodhan, M. A. (2025). blastdbbuilder: Building a Customised BLASTn Database. https://doi.org/10.5281/zenodo.17394137

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Support

For issues, bug reports, or feature requests, please contact: Asad Prodhan. E-mail: [e-mail], [e-mail]