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Read Depth Analysis to Identify CNV in Bacteria Using CNOGpro

  • Ola BrynildsrudEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)

Abstract

Whole-genome sequencing with short-read technologies is well suited for calling single nucleotide polymorphisms, but has major problems with the detection of structural variants larger than the read length. One such type of variation is copy number variation (CNV), which entails deletion or duplication of genomic regions, and the expansion or contraction of repeated elements. Duplicated and deleted regions will typically be collapsed during de novo assembly of sequence data, or ignored when mapping reads toward a reference. However, signatures of the copy number variation can be detected in the resultant read depth at each position in the genome. We here provide instructions on how to analyze this read depth signal with the R package CNOGpro, allowing for estimation of copy numbers with uncertainty for each feature in a genome.

Key words

Read depth CNV Bacteria CNOGpro Coverage Whole-genome sequencing 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Norwegian Institute of Public HealthOsloNorway

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