Package: sideretro (1.1.6-2)

[ Source: sideretro  ]

pipeline for detecting Somatic Insertion of DE novo RETROcopies

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.

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.

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).

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  dep: libc6 (>= 2.41) [sh4]

• dep: libc6.1 (>= 2.38) [alpha]

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• dep: libhts3t64 (>= 1.17)

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Architecture	Package Size	Installed Size	Files
alpha (unofficial port)	84.3 kB	246.0 kB	[list of files]
amd64	88.4 kB	232.0 kB	[list of files]
arm64	90.2 kB	245.0 kB	[list of files]
armel	80.8 kB	243.0 kB	[list of files]
armhf	79.4 kB	179.0 kB	[list of files]
i386	93.1 kB	247.0 kB	[list of files]
m68k (unofficial port)	79.7 kB	211.0 kB	[list of files]
ppc64el	92.5 kB	309.0 kB	[list of files]
riscv64	96.6 kB	217.0 kB	[list of files]
sh4 (unofficial port)	91.3 kB	243.0 kB	[list of files]
x32 (unofficial port)	89.2 kB	223.0 kB	[list of files]