ABySS Explorer: Visualizing Genome Sequence Assemblies

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ABySS Explorer Visualizing Genome Sequence
Assemblies
Cydney B. Nielsen, Shaun D. Jackman, Inanc
Birol, and Steven J.M. Jones
Presented by Andrew Trusty
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Motivation
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Related Work
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Related Work

• UCSC Browser

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• Ensembl Browser

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Related Work

• Consed/Phrapview

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Related Work

• gap4

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Related Work

• EagleView

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Related Work

• Hawkeye

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Related Work

• ConPath

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Design Process
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Analyst Needs
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AbySS Explorer Design Focus
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Connectivity Overlap

• The de Bruijn graph of a collection of reads.
• The actual relationship between the reads
• The inversion of the de Bruijn graph. Edges are
  k-mers, and nodes represent k 1 overlap.

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Contig Coverage
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Read Pairs

• Pair alignment
• 2 linked contigs highlighted in blue and
  connected by a dotted link.
• Can infer path from unambiguous read pair info

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Structural Viz
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Metadata Annotation
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Future
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Drawbacks
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fin
many slides liberally borrowed from a
presentation by Adam D Smith
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