Exploring 50 Whole Genomes with Chromium Linked Reads
Dr. Chris Whelan
Tuesday, November 29, 2016
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Chapters
Introduction
Unlinked-Reads: short range information
Generating linked reads
Linked-Reads: long range information
The InPSYght project and linked reads
A pilot to test linked reads
Standard Short Read Alignment
Long Ranger – LariatTM Aligner
Barcode Aware Alignment
Differential Coverage
Long Range Phasing
SNP and INDEL calling
Structural Variation Detection
Deletion Revealed with Phased Reads
Linked Reads in Structural Variation Calling
Linked reads make larger SVs visible pt.1
Linked reads make larger SVs visible pt.2
Linked reads make larger SVs visible pt.3
Dispersed Duplications
Dispersed Duplication Example
De novo Assembly
Summary and Next Steps
Acknowledgements
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