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

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 combine the DNA sequence data from multiple organs. TRACESPipe relies on cooperation between three modalities: compression-based prediction, sequence alignment, and <i>de-novo</i> assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. <br>TRACESPipe performed outstandingly when tested on synthetic and <i>ex-vivo</i> 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.<br> TRACESPipes uniqueness to process and analyze simultaneously 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. <br>Moreover, additional features such as DNA damage estimation, mitochondrial DNA reconstruction and analysis, and exogenous-source controls expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. <br>TRACESPipe is released under GPLv3 and is openly available to download from GitHub.