V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
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Date
2023-10-16
Publication Type
Working Paper
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yes
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Abstract
The large amount and diversity of viral genomic datasets generated by next-generation sequencing technologies poses a set of challenges for computational data analysis workflows, including rigorous quality control, adaptation to higher sample coverage, and tailored steps for specific applications. Here, we present V-pipe 3.0, a computational pipeline designed for analyzing next-generation sequencing data of short viral genomes. It is developed to enable reproducible, scalable, adaptable, and transparent inference of genetic diversity of viral samples. By presenting two large-scale data analysis projects, we demonstrate the effectiveness of V-pipe 3.0 in supporting sustainable viral genomic data science.
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published
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Cold Spring Harbor Laboratory
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Subject
Next-generation sequencing; Data processing; Sustainable workflow; Benchmark; Global haplotype reconstruction
Organisational unit
03790 - Beerenwinkel, Niko / Beerenwinkel, Niko
09490 - Stadler, Tanja / Stadler, Tanja
02892 - NEXUS Personalized Health / NEXUS Personalized Health
Notes
Funding
955974 - Understanding (harmful) virus-host interactions by linking virology and bioinformatics (EC)
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