SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences

Abstract

Summary: Controlled modification of sequencing data is important for reproducible benchmarking, particularly when evaluating analyses affected by read fragmentation, divergent reference genomes and ancient DNA damage. SCAR introduces controlled mutations, fragmentation and position-specific damage into FASTA and FASTQ data. All features can be used separately or in combination, and empirical fragment-length and mismatch profiles can be supplied to closely reproduce the properties of targeted datasets. Validation analyses showed the successful implementation of the requested sequence changes, and their impact on read mapping and heterozygosity analyses. Availability and Implementation: SCAR is implemented in C++ and the latest code is available at https://github.com/Madshartmann1/SCAR. The version described in this article is archived at Zenodo at https://doi.org/10.5281/zenodo.22789736 , with validation material available at https://doi.org/10.5281/zenodo.21915766.