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kishwarshafin committed Mar 8, 2021
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<img src="./img/PMDV_variant_calling_ONT.png" alt="PEPPER-Margin-DeepVariant Variant Calling Workflow" width="720p"></img>
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### How to cite
If you use `PEPPER-Margin-DeepVariant` please cite the following manuscript:
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### Methods and results
A detailed description of `PEPPER-Margin-DeepVariant` methods and results are discussed in the following manuscript:


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<summary><a href="https://www.biorxiv.org/content/10.1101/2021.03.04.433952v1"><b>bioRxiv:</b> Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks.</a></summary>
Authors: Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, <br/> Gunjan Baid, Jordan M Eizenga, Karen H Miga, Paolo Carnevali, Miten Jain, Andrew Carroll, Benedict Paten.
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### Quickstart
Please follow the quickstart guides to assess your setup. Please follow case-study documentations for detailed instructions.
* **Docker**: [Oxford Nanopore and PacBio HiFi variant calling quick start](./docs/quickstart/variant_calling_docker_quickstart.md).
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