useR! 2024

Aberrant repair of DNA double strand breaks is a prominent feature of various cancers. It can result in deletions, duplications, translocations and insertions. In our previous work, we analyzed amplicon-sequencing data with our custom pipeline to detect templated insertions at the DNA damage sites (Akimova et al. 2021, doi:10.1093/nar/gkab051). Here we present the dupseqr, an R package, which summarizes several functions for a sequential tracing of insertions, duplications and inversions. Dupseqr comprises, on the one hand, the existing bash commands in a pipe function for the pre-processing of the FASTQ files and BLAST search, followed by precise trimming and filtering of mapped sequences in order to identify insertions. On the other hand, it includes a novel function to detect and depict duplications and inversions directly from your DNA sequences, whereas the input and the output can be adjusted depending on your initial data structure and your final goal. All in all, dupseqr provides a quick possibility to elucidate aberrations, such as short duplications, inversions and insertions from distant genomic sites using the sequencing data.