genome_assembly_pipeline

This is an integrated pipeline for eukaryotic genome assembly and gene annotation. It currently supports PacBio HiFi reads and RNA-seq reads, both of which are required as inputs. See this page for details on the expected outputs.

Requirements

Before running the workflow, make sure the following software is installed:

• Snakemake ≥ 9.0.0
• Apptainer (Singularity)

Getting Started

Follow the steps below to set up and run the workflow:

1. Clone the Repository

Clone this repository to your local machine:

git clone https://github.com/mkrg01/genome_assembly_pipeline.git
cd genome_assembly_pipeline

2. Prepare Input Files and Configure Settings

See config/README.md for details on preparing input files and adjusting configuration parameters.

3. Execute the Workflow

Run the workflow from the repository root directory. Replace /path/to/repo with the actual path to your local repository:

cd /path/to/repo
snakemake --sdm conda apptainer --singularity-args "--bind $(pwd)" --cores 64 all

Tip

You can run the pipeline in a stepwise manner. Replace all with one of the command below.

1. assembly_all: Runs rules up to the generation of the Hifiasm assembly and its associated metrics.
2. remove_organelle_all: Runs rules up to the organelle removal step and its associated metrics.
3. remove_contamination_all: Runs rules up to the contamination removal step by FCS and its associated metrics.
4. softmask_all: Runs rules up to softmasking by RepeatMasker.
5. gene_prediction_all: Runs rules up to gene prediction and related metrics (equivalent to all).

You do not need to start from step 1 — for example, if you run remove_contamination_all first, the rules related to assembly_all and remove_organelle_all will be executed automatically.

Note

Adjust the --cores value based on your available computational resources.

Note

All rules except those with FCS wrapper scripts (fcs.py, run_fcsadaptor.sh) run in containers. These wrapper scripts internally call the main FCS functions, which are executed inside containers.

The output will be generated in the results directory.