Apr 2, 2020

BAdabouM: a genomic structural variations discovery tool for polymorphism analyses

BioRxiv : the Preprint Server for Biology
Tolutope Oluseyi AkejuFrederic Boyer

Abstract

Genomic Structural Variations (SVs) are known to impact the evolution of genomes and to have consequences on individual's fitness. Nevertheless, they remain challenging to detect in whole genome re-sequencing (WGS) data. Lots of methods detecting SVs are described in the literature but they might be hard to install, have non-trivial settings, do not detect all SVs categories and have generally high levels of false positive. Here we introduce BAdabouM, a fast (C written) and easy to install SVs discovery tool. BAdabouM auto evaluates read length, library size and mean coverage to set thresholds specific to each experiment. BAdabouM interprets multiple SVs signatures (reads aligned with a split, non-concordant mapped pairs or uneven coverage) to detect insertions, deletions, copy number variations, inversions, and translocations at single-nucleotide resolution. When compared with two widely used methods on simulated and real datasets, BAdabouM was faster, exhibited a similar accuracy with a good concordance on SVs detected, and detected significantly more insertions. BAdabouM was more reproducible to detect independently SVs across individuals, which is a clear advantage when characterizing population polymorphism. Furthermore, B...Continue Reading

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Mentioned in this Paper

Antibiotic throat preparations
Antifungal Antibiotics, Topical
Coliform bacteria
Cell Count
Operator of Medical Device
Antibiotics, Gynecological
Isolate compound
Disease Transmission
Biochemical Reaction
Oncogene protein E4, human papilloma virus type 1

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