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

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 fur

SUBMITTER: Schwarz PM 

PROVIDER: S-EPMC10941317 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature