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Update README.md
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alihamraoui authored Jun 25, 2024
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Expand Up @@ -103,14 +103,6 @@ nextflow run main.nf --matrix test_data/matrix.csv \
--transcriptome test_data/transcriptome.fa
```

## example 2:
```bash
nextflow run main.nf --matrix test_data/matrix.csv \
--bc_counts test_data/test_bc.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.
Expand All @@ -124,7 +116,7 @@ nextflow clean -f
```
## Acknowledgements

- We would like to express our gratitude to [Youyupei](https://github.com/youyupei) for the development of [SLSim](https://github.com/youyupei/SLSim), which has been foundational to the `AsaruSim` workflow.
- We would like to express our gratitude to [Youyupei](https://github.com/youyupei) for the development of [SLSim](https://github.com/youyupei/SLSim), which has been helpful to the `AsaruSim` workflow.
- Additionally, our thanks go to the teams behind [Badread](https://github.com/rrwick/Badread) and [SPARSim](https://gitlab.com/sysbiobig/sparsim), whose tools are integral to the `AsaruSim` workflow.

## Support and Contributions
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