2022
DOI: 10.1038/s41598-022-17318-5
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Using HPV-meta for human papillomavirus RNA quality detection

Abstract: In the era of cervical cancer elimination, accurate and validated pipelines to detect human papillomavirus are essential to elucidate and understand HPV association with human cancers. We aimed to provide an open-source pipeline, “HPV-meta”, to detect HPV transcripts in RNA sequencing data, including several steps to warn operators for possible viral contamination. The “HPV-meta” pipeline automatically performs several steps, starting with quality trimming, human genome filtering, HPV detection (blastx), cut-o… Show more

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Cited by 2 publications
(3 citation statements)
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“…Pseudo-anonymised data can furthermore enrich datasets to train and validate machine learning models to classify or predict cervical cancer and all metagenomics analysis pipelines developed by studies on the Cervical Screening Cohort 17 , 18 are open source. These pipelines can thus enrich other datasets with evidence based on metagenomics approaches.…”
Section: Background and Summarymentioning
confidence: 99%
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“…Pseudo-anonymised data can furthermore enrich datasets to train and validate machine learning models to classify or predict cervical cancer and all metagenomics analysis pipelines developed by studies on the Cervical Screening Cohort 17 , 18 are open source. These pipelines can thus enrich other datasets with evidence based on metagenomics approaches.…”
Section: Background and Summarymentioning
confidence: 99%
“…Sequencing data and metadata are uploaded interactively or through Jupyter notebooks to facilitate metadata uploading and use. The published bioinformatics pipelines for metagenomics analyses, available through GitHub 17 , 18 , are also implemented in the Hopsworks platform at Karolinska Institutet. In-house developed JAVA-based management tools for self-testing, reporting and data extraction for research.…”
Section: Data Recordsmentioning
confidence: 99%
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