Abstract
BackgroundAdvances 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.FindingsTRACESPipe 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.ConclusionsTRACESPipe’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.
Highlights
The field of virology has experienced a revolution along with the introduction of next-generation sequencing technologies (NGS) as the number of emerging and newly discovered viruses continues to rise at near-exponential rates
We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs
Thanks to NGS, long-standing questions on the virome and on its interactions with the host can be investigated. These include the study of the types and genetic diversities of the viral populations residing in different organs of the human body [1]
Summary
The field of virology has experienced a revolution along with the introduction of next-generation sequencing technologies (NGS) as the number of emerging and newly discovered viruses continues to rise at near-exponential rates. Thanks to NGS, long-standing questions on the virome and on its interactions with the host can be investigated These include the study of the types and genetic diversities of the viral populations residing in different organs of the human body [1]. For processing of virus sequencing data, several pipelines exist (e.g., VIP [2], VirFinder [3], ViromeScan [4], HoloVir [5], iVirus [6], VirMAP [7], FastViromeExplorer [8], and GenomeDetective [9]) These tools are not optimized for the analysis of data derived from multiple organs, leaving each tissue to be analysed individually and independently, at the expense of much computational time. Additional features include secure transmission and storage of sensitive data, quality controls, DNA damage estimation, and human Y-chromosome analysis
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