2025/08/01 by Claire C. Menard, Nathan S. Catlin, Adrian E. Platts +6 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #Plant Disease Resistance and Genetics #Genomics and Phylogenetic Studies
paper · pdf · doi:10.1101/2025.07.30.667279
openalex publication_date 2025/08/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22
ABSTRACT Transposable element (TE) insertion polymorphisms (TIPs) are TEs not in the same location between individuals. TIPs have contributed to genomic and phenomic variation but have been historically difficult to study due to their repetitive nature. Here, we describe a fast and memory-efficient tool to identify novel TIPs from short read sequences. SWIF-TE was able to identify 1,438 insertions at a precision rate of 27% using 0.10 Gb of memory and 0.82 hours of runtime from 15x resequencing data of a non-reference maize inbred. SWIF-TE is a powerful tool for studying TE variation in species with TE-rich genomes.