YMAP: A pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Darren A. Abbey, Jason Funt, Mor N. Lurie-Weinberger, Dawn A. Thompson, Aviv Regev, Chad L. Myers, Judith Berman*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The YMAP pipeline ( http://lovelace.cs.umn.edu/Ymap/ ) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes.

Original languageEnglish
Article number100
Pages (from-to)1-15
Number of pages15
JournalGenome Medicine
Volume6
DOIs
StatePublished - 20 Nov 2014

Funding

FundersFunder number
National Science FoundationDBI 0953881
National Institutes of HealthT32GM007287
Howard Hughes Medical Institute
National Institute of Allergy and Infectious DiseasesR01 AI-0624273
Burroughs Wellcome Fund
Seventh Framework Programme303635
FP7 People: Marie-Curie Actions
European Research Council340087
Human Frontier Science Program
Seventh Framework Programme

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