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Whole-Genome Shotgun Sequence CNV Detection Using Read Depth

  • Fatma Kahveci
  • Can AlkanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)

Abstract

With the developments in high-throughput sequencing (HTS) technologies, researchers have gained a powerful tool to identify structural variants (SVs) in genomes with substantially less cost than before. SVs can be broadly classified into two main categories: balanced rearrangements and copy number variations (CNVs). Many algorithms have been developed to characterize CNVs using HTS data, with focus on different types and size range of variants using different read signatures. Read depth (RD) based tools are more common in characterizing large (>10 kb) CNVs since RD strategy does not rely on the fragment size and read length, which are limiting factors in read pair and split read analysis. Here we provide a guideline for a user friendly tool for detecting large segmental duplications and deletions that can also predict integer copy numbers for duplicated genes.

Key words

Copy number variation Whole genome shotgun sequencing Read depth mrFAST mrsFAST 

Abbreviations

CNV

Copy number variation

mrCaNaVaR

Micro read Copy Number Variant Regions

mrFAST

Micro read Fast Alignment Search Tool

mrsFAST

Micro read substitution only Fast Alignment Search Tool

RD

Read depth

TRF

Tandem repeat finder

WGS

Whole genome sequencing

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Computer EngineeringBilkent UniversityAnkaraTurkey

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