SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines.

ABSTRACT:

Background

Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of pathogens is being recognized, for example, Helicobacter pylori and human papillomavirus in the cases of gastric non-cardia and cervical carcinomas, respectively. As of yet, no benchmark has been carried out on the performance of computational approaches for bacterial and viral detection within host-dominated sequence data.

Results

We present the results of benchmarking over 70 distinct combinations of tools and parameters on 100 simulated cancer datasets spiked wit

SUBMITTER: Gihawi A 

PROVIDER: S-EPMC6805339 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature