SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences
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…
Controlled modification of sequencing data is crucial for reproducible benchmarking, especially when assessing analyses influenced by read fragmentation, genetic differences between reference genomes, and DNA damage from ancient sources. SCAR offers controlled mutations, fragmentation, and position-specific damage to FASTA and FASTQ data.
These features can be utilized individually or in combination, with empirical fragment-length and mismatch profiles available to replicate the characteristics of specific datasets accurately. Validation studies confirmed the successful implementation of these sequence alterations, along with their effect on read mapping and heterozygosity analyses.
SCAR is developed in C++ and its most recent code is accessible at https://github.com/Madshartmann1/SCAR. The version discussed in this article is preserved at Zenodo, accessible at https://doi.org/10.5281/zenodo.22789736, with validation data available at https://doi.org/10.5281/zenodo.21915766.
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