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Description

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.

Repository

https://github.com/giesselmann/nanopype

Project Slug

nanopype

Last Built

1 month ago passed

Maintainers

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Tags

pipeline, snakemake, high-throughput, minion, nanopore-sequencing, oxford-nanopore

Short URLs

nanopype.readthedocs.io
nanopype.rtfd.io

Default Version

latest

'latest' Version

master