Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli
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Background Discordant read pairs [1,2] – those deviating either from expected insert size range or correct relative orientation – have served as vital clues to identifying structural variants (SV) in genomes. Collecting discordant read pairs is the first step in SV detection and is often done by sequence alignment. When there are repetitive elements, such as insertion sequence (IS), a class of transposable elements in bacterial genomes, discordant read pairs can have multiple mapping loci – making them more challenging to be placed and interpreted. Instead of resolving such tangled mapping results, many tools simply ignore these mapped read pairs, potentially missing SVs involving repetitive elements.
[1] E. Eichler,et al. Fine-scale structural variation of the human genome , 2005, Nature Genetics.
[2] Haixu Tang,et al. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing , 2012, Proceedings of the National Academy of Sciences.
[3] Martin Strauch,et al. Reconstructing Tumor Genome Architectures , 2022 .
[4] Haixu Tang,et al. De novo repeat classification and fragment assembly , 2004, RECOMB.