A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level

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Pratas , D , Toppinen , M , Pyöriä , L , Hedman , K , Sajantila , A & Perdomo , M F 2020 , ' A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level ' , GigaScience , vol. 9 , no. 8 , 086 . https://doi.org/10.1093/gigascience/giaa086

Title: A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level
Author: Pratas, Diogo; Toppinen, Mari; Pyöriä, Lari; Hedman, Klaus; Sajantila, Antti; Perdomo, Maria F.
Contributor: University of Helsinki, Department of Virology
University of Helsinki, Klaus Hedman / Principal Investigator
University of Helsinki, Virus infections and immunity
University of Helsinki, HUSLAB
University of Helsinki, Department of Forensic Medicine
University of Helsinki, Virus infections and immunity
Date: 2020-08
Language: eng
Number of pages: 11
Belongs to series: GigaScience
ISSN: 2047-217X
URI: http://hdl.handle.net/10138/320311
Abstract: Background: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. Findings: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. Conclusions: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.
Subject: efficient pipeline
multi-organ sequencing
viral genomes
genome analysis
parvovirus B19
JC polyomavirus
mitochondrial DNA
3111 Biomedicine

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