DeepClone, an end-to-end protocol to study somatic mutagenesis and selection at high resolution v2

The advent of Next Generation Sequencing (NGS) technologies opened up the door to the study of somatic mutagenesis and selection through the analysis of a salient clone in a sample, as in the case of cancer. This was made possible by the development of an ecosystem of computational methods that enabled mutation calling, the study of mutational processes, and the quantification of positive selection, among other research avenues. Recently, the introduction of DNA duplex sequencing technologies has allowed the detection of somatic mutations that occur in one or few cells in a sample. This has unlocked the possibility to study the interplay between mutagenesis and selection on hundreds or thousands of clones per sample, providing access to understanding somatic evolution in scenarios that were not previously easy to access, such as normal tissues. The adoption of DNA duplex sequencing technologies has been hindered, among other reasons, by the lack of a complete ecosystem of computational tools that support end-to-end analysis from the sequencing raw data to the quantification of multiple aspects of mutagenesis and selection. To overcome this problem, we present DeepClone, a protocol that comprises an experimental DNA duplex sequencing library preparation solution, and two computational pipelines to readily identify somatic mutations, and carry out calculations of mutagenesis and selection in a cohort of samples. Find the code for the data processing steps here: https://github.com/bbglab/deepUMIcaller https://github.com/bbglab/deepCSA