Asaru Sim Documentation

AsaruSim is an automated Nextflow workflow designed for simulating 10x single-cell Nanopore reads. It allows to benchmark and optimize single-cell Nanopore long read data processing pipelines.

Prerequisites

Before starting, ensure the following tools are installed and properly set up on your system:

• Nextflow: A workflow engine for complex data pipelines. Installation guide for Nextflow.
• Docker or Singularity: Containers for packaging necessary software, ensuring reproducibility. Docker installation guide, Singularity installation guide.
• Git: Required to clone the workflow repository. Git installation guide.

Installation

Clone the AsaruSim GitHub repository:

git clone https://github.com/alihamraoui/AsaruSim.git
cd AsaruSim

Configuration

Customize runs by editing the nextflow.config file and/or specifying parameters at the command line.

Pipeline Input Parameters

Here are the primary input parameters for configuring the workflow:

Parameter	Description	Default Value
matrix	Path to the count matrix csv file (required)	test_data/matrix.csv
bc_counts	Path to the barcode count file	test_data/test_bc.csv
transcriptome	Path to the reference transcriptome file (required)	test_data/transcriptome.fa
features	Matrix feature counts	transcript_id
gtf	Path to transcriptom annotation .gtf file	null
cell_types_annotation	Path to cell type annotation .csv file	null

Error/Qscore Parameters

Configuration for error model:

Parameter	Description	Default Value
trained_model	Badread pre-trained error/Qscore model name	nanopore2023
badread_identity	Comma-separated values for Badread identity parameters	"98,2,99"
error_model	Custom error model file (optional)	null
qscore_model	Custom Q-score model file (optional)	null
build_model	to build your own error/Qscor model	false
model_fastq	reference real read (.fastq) to train error model (optional)	false
ref_genome	reference genome .fasta file (optional)	false

Additional Parameters

Parameter	Description	Default Value
amp	Amplification factor	1
outdir	Output directory for results	"results"
projectName	Name of the project	"test_project"

Run Parameters

Configuration for running the workflow:

Parameter	Description	Default Value
threads	Number of threads to use	4
container	Docker container for the workflow	'hamraouii/wf-SLSim'
docker.runOptions	Docker run options to use	'-u $(id -u):$(id -g)'

Execution

To run the workflow with basic example:

You can simulate a realistic disribution of per barcodes UMI counts by providing in addition to the filtered counts matrix a .csv file of BC counts. AsaruSim will add a random transcrips count to fit the real distribution.

nextflow run main.nf --matrix test_data/matrix.csv \
                     --bc_counts test_data/test_bc.csv \
                     --transcriptome test_data/transcriptome.fa \

User can choose among 4 ways to simulate template reads.

• use a real count matrix
• estimated the parameter from a real count matrix to simulate synthetic count matrix
• specified by his/her own the input parameter
• a combination of the above options

We use SPARSIM tools to simulate count matrix. for more information a bout synthetic count matrix, please read SPARSIM documentaion.

use a real count matrix

nextflow run main.nf --matrix test_data/matrix.csv \
                     --transcriptome test_data/transcriptome.fa

Results

After execution, results will be available in the specified --outdir. This includes simulated Nanopore reads .fastq, along with log files and QC report.

Cleaning Up

To clean up temporary files generated by Nextflow:

nextflow clean -f

Acknowledgements

• We would like to express our gratitude to Youyupei for the development of SLSim, which has been helpful to the AsaruSim workflow.
• Additionally, our thanks go to the teams behind Badread and SPARSim, whose tools are integral to the AsaruSim workflow.

Support and Contributions

For support, please open an issue in the repository's "Issues" section. Contributions via Pull Requests are welcome. Follow the contribution guidelines specified in CONTRIBUTING.md.

License

AsaruSim is distributed under a specific license. Check the LICENSE file in the GitHub repository for details.