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  Nanopype: A modular and scalable nanopore data processing pipeline

Giesselmann, P., Hetzel, S., Müller, F.-J., Meissner, A., & Kretzmer, H. (2019). Nanopype: A modular and scalable nanopore data processing pipeline. Bioinformatics, 2019: btz461. doi:10.1093/bioinformatics/btz461.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-A985-7 Version Permalink: http://hdl.handle.net/21.11116/0000-0004-AC69-5
Genre: Journal Article

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 Creators:
Giesselmann, Pay1, Author              
Hetzel, Sara1, Author              
Müller, Franz-Josef2, Author              
Meissner, Alexander1, Author              
Kretzmer, Helene1, Author              
Affiliations:
1Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2379694              
2Cellular Phenotyping (Franz-Josef Müller), Dept. of Genome Regulation, (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_3014190              

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 Abstract: Long-read third-generation nanopore sequencing enables researchers to now address a range of questions that are difficult to tackle with short read approaches. The rapidly expanding user base and continuously increasing throughput have sparked the development of a growing number of specialized analysis tools. However, streamlined processing of nanopore datasets using reproducible and transparent workflows is still lacking. Here we present Nanopype, a nanopore data processing pipeline that integrates a diverse set of established bioinformatics software while maintaining consistent and standardized output formats. Seamless integration into compute cluster environments makes the framework suitable for high-throughput applications. As a result, Nanopype facilitates comparability of nanopore data analysis workflows and thereby should enhance the reproducibility of biological insights.

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Language(s): eng - English
 Dates: 2019-06-072019-06-13
 Publication Status: Published online
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 2019 Sequence Number: btz461 Start / End Page: - Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991