A bioinformatic pipeline for simulating viral integration data.

ABSTRACT: Viral integration is a complex biological process, and it is useful to have a reference integration dataset with known properties to compare experimental data against, or for comparing with the results from computational tools that detect integration. To generate these data, we developed a pipeline for simulating integrations of a viral or vector genome into a host genome. Our method reproduces more complex characteristics of vector and viral integration, including integration of sub-genomic fragments, structural variation of the integrated genomes, and deletions from the host genome at the integration site. Our method [1] takes the form of a snakemake [2] pipeline, consisting of a Python [3] script using the Biopython [4] module that simulates integrations of a viral reference into a host

SUBMITTER: Scott S 

PROVIDER: S-EPMC9046613 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature