sideretro - 1.1.6-2 main

sideRETRO is a bioinformatics tool designed for the detection of somatic
retrocopy insertions, also known as retroCNVs, in whole genome sequencing
(WGS) and whole exome sequencing (WES) data.
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Retrocopies, also known as processed pseudogenes, are sequences derived
from protein-coding genes, generated by the duplication of these genes
through the transposition of their mature messenger RNA via the LINE-1
enzymatic machinery. Retrocopies can be fixed, meaning they are present
in all genomes of a given species (including the species' reference
genome), or unfixed (polymorphic, germline, or somatic), in which case
they are referred to as retroCNVs. While fixed retrocopies have received
considerable attention in the scientific community, knowledge of retroCNVs
remains limited, largely due to the lack of specialized bioinformatics
tools for their identification and annotation in DNA sequencing data.
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sideRETRO is a dedicated computational algorithm that detects retrocopies
absent from the reference genome but present in WGS and WES data from
other individuals. In addition to identifying retroCNVs, sideRETRO annotates
several characteristics associated with these events. It provides information
on the genomic coordinates of the insertion, including chromosome, insertion
point, and DNA strand. It also determines the genomic context of the event
(exonic, intronic, or intergenic), performs genotyping (presence or absence),
and provides haplotyping information (homozygous or heterozygous).