HolmGenome Pipeline

HolmGenome is a one-step pipeline that performs assembly, quality control, and annotation of bacteria genomic data. It takes raw sequencing reads and produces a fully annotated genome in a single run.

Features

• Assembly: Uses SPAdes to assemble raw reads.
• QC: Employs Trimmomatic & FastQC for trimming and quality checks.
• Annotation: Runs Prokka to annotate assembled contigs.

Installation

Requirements

• Python Version: Python 3.6 or higher
• External Dependencies:
• FastQC: 0.12.0
• Trimmomatic: 0.39
• SPAdes: 3.15.4
• Prokka: 1.14.5
• BBMap: 38.86
• QUAST: 5.2.0

Development Version

```bash git clone https://github.com/TiffanyFeng08/HolmGenome.git

```

Check the environment before using (recommended)

cd HolmGenome python HolmGenome.py --check

Usage

HolmGenome.py will detect all *.fastq or *.fastq.gz files in a directory and run on each sample it can pair

``` Usage: HolmGenome.py [OPTIONS] options: -h, --help show help message and exit -i INPUT, --input INPUT Path to the input directory -o OUTPUT, --output OUTPUT Path to the output directory --trimmomaticpath TRIMMOMATICPATH Path to the Trimmomatic executable or JAR --adapterspath ADAPTERSPATH Path to the adapters file --prokkadbpath PROKKADBPATH Path to the Prokka database --mincontiglength MINCONTIGLENGTH Minimum contig length (default: 1000) --check Check if all dependencies are installed -v, --version Show the pipeline version number and exit

```

python HolmGenome.py -i INPUT -o OUTPUT --trimmomatic_path TRIMMOMATIC_PATH --adapters_path ADAPTERS_PATH --prokka_db_path PROKKA_DB_PATH

Example bash script

```

!/bin/bash

SBATCH --account=your_account

SBATCH --time=5:00:00

SBATCH --job-name=HolmGenome

SBATCH --nodes=1

SBATCH --ntasks=1

SBATCH --mem-per-cpu=5G

SBATCH --cpus-per-task=4

SBATCH --mail-user=your.email@somemail.com

SBATCH --mail-type=BEGIN,END,FAIL,REQUEUE

module load StdEnv/2020 gcc/9.3.0 module load python/3.10.2 module load scipy-stack/2022a module load fastqc/0.12.0 module load trimmomatic/0.39 module load spades/3.15.4 module load prokka/1.14.5 module load bbmap/38.86 module load quast/5.2.0 source ~/HolmGenome/bin/activate

python HolmGenome.py -i /path/to/data -o /path/to/output \ --trimmomaticpath /path/to/trimmomatic-0.39.jar \ --adapterspath /path/to/adapters.fa \ --prokkadbpath /path/to/prokka_db ```