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Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

RepairNatrix: a Snakemake workflow for processing DNA sequencing data for DNA storage

Peter Michael Schwarz¹, Marius Welzel¹, Dominik Heider¹

¹Department of Mathematics and Computer Science, University of Marburg, Marburg 35032, Germany.

Bioinformatics Advances

|March 18, 2024

Abstract

Motivation:

There has been rapid progress in the development of error-correcting and constrained codes for DNA storage systems in recent years. However, improving the steps for processing raw sequencing data for DNA storage has a lot of untapped potential for further progress. In particular, constraints can be used as prior information to improve the processing of DNA sequencing data. Furthermore, a workflow tailored to DNA storage codes enables fair comparisons between different approaches while leading to reproducible results.

Results:

We present RepairNatrix, a read-processing workflow for DNA storage. RepairNatrix supports preprocessing of raw sequencing data for DNA storage applications and can be used to flag and heuristically repair constraint-violating sequences to further increase the recoverability of encoded data in the presence of errors. Compared to a preprocessing strategy without repair functionality, RepairNatrix reduced the number of raw reads required for the successful, error-free decoding of the input files by a factor of 25-35 across different datasets.

Availability And Implementation:

RepairNatrix is available on Github: https://github.com/umr-ds/repairnatrix.

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