Shaun Jackman

Thesis Committee

University Examiners

Previous committee meeting 2018-03-14

Selected Papers

• Assembly of the complete Sitka spruce chloroplast… L Coombe, RL Warren, SD Jackman, C Yang, BP Vandervalk, …, I Birol
  PloS one 2016
• Spaced seed data structures for de novo assembly
  I Birol, J Chu, H Mohamadi, SD Jackman, K Raghavan, …, RL Warren
  International journal of genomics 2015
• Konnector v2.0: pseudo-long reads from PE sequencing
  BP Vandervalk, C Yang, Z Xue, K Raghavan, J Chu, H Mohamadi, SD Jackman, …, I Birol
  BMC medical genomics 2015
• Sealer: a scalable gap-closing application…
  D Paulino, RL Warren, BP Vandervalk, A Raymond, SD Jackman, I Birol
  BMC Bioinformatics 2015
• On the representation of de Bruijn graphs
  R Chikhi, A Limasset, SD Jackman, JT Simpson, P Medvedev
  Journal of Computational Biology 2015
• Improved white spruce (Picea glauca) genome…
  RL Warren, CI Keeling, MMS Yuen, A Raymond, GA Taylor, …, J Bohlmann
  The Plant Journal 2015
• Assembling the 20Gb white spruce genome…
  I Birol, A Raymond, SD Jackman, S Pleasance, R Coope, …, SJM Jones
  Bioinformatics 2013

Papers

• Four first-author (or joint) papers
• One paper each year from 2015 through 2018
• Collaborated on 32 papers since 2009
• 28 papers with at least 10 citations
• One first-author manuscript in review (ORCA)
• One first-author manuscript in preparation
  (Sitka spruce mitochondrion)
• ABySS has been cited over 2,700 times!

Manuscripts

• ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research SD Jackman^*, T Mozgacheva^*, S Chen, B O’Huiginn, L Bailey, I Birol, SJM Jones
  (in review)
• Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure SD Jackman, L Coombe, RL Warren, …, J Bohlmann, SJM Jones, Inanc Birol

Efficient Assembly
of Large Genomes

1. Introduction
2. ABySS 2.0
3. Tigmint
4. UniqTag
5. ORCA
6. Organellar genomes of white spruce
7. Mitochondrial genome of Sitka spruce
8. Genome assembly of western redcedar
9. Conclusion

ABySS 2.0

• Implemented Bloom filter de Bruijn Graph
  • Konnector and Konnector 2.0 with Ben Vandervalk
  • Sealer with Daniel Paulino
  • ABySS 2.0 with Ben Vandervalk
• Reduce memory usage by twelve fold over ABySS 1.0
• Assemble a conifer genome with a single machine
• Memory usage is independent of parameter k
• Assembled a human genome with ABySS 2.0 (35 GB RAM)

ABySS 2.0

• Compared to ABySS 1.5 and six other assemblers
• Submitted genome assemblies to NCBI
• Published paper in Genome Research (2017)
• Presented a talk at RECOMB-Seq 2018

Correcting misassemblies using linked reads

• Incorrectly assembled sequence complicates all downstream analyses
• Misassemblies also limit contiguity
• Cut contigs where linked reads and assembly disagree
• Tigmint + ARCS improved contiguity two fold over ARCS alone in human from 8 Mbp to 16 Mbp scaffold NGA50
• Further developed the tool with Lauren Coombe
• Presented a talk and poster at RECOMB-Seq 2018

UniqTag

Assign unique and stable gene identifiers
to genes based on their sequence content

Background

• Genes without function identified by serial number
• One small changes causes a complete renumbering
• Inconvenient when gene identifiers change
  between assembly versions

UniqTag

• Genes with unchanged coding sequence have
  stable identifiers between assembly versions
• Published paper in PLOS ONE (2015)

ORCA

• Comprehensive bioinformatics computing environment
• Includes hundreds of bioinformatics tools
  in a single easily-installed Docker image
  (all tools available to the Homebrew package manager)
• Useful for education and research

Use Cases

• External collaborators of BC Cancer
• Hackseq genomics hackathon (https://hackseq.com)
• Undergraduate class on bioinformatics at UBC

White Spruce Organelles

• Assembled cpDNA and mtDNA genomes
• Annotated genes (mRNA, rRNA, tRNA) and repeats
• Analysed RNA-seq data to quantify
  • transcript abundance in eight tissues
  • expressed ORFs
  • C-to-U RNA editing
  • cryptic ACG start codons due to C-to-U RNA editing
• Submitted annotated genomes to GenBank
• Published paper in Genome Biology and Evolution (2015)

Sitka Spruce Mitochondrion Methods

• 11 lanes of Oxford Nanopore Sequencing
• 5x nuclear coverage
• 26x mitochondrial coverage
• 10x Genomics Chromium sequencing
• 59x mitochondrial coverage in one lane
• Assemble Nanopore reads
• Polish with linked reads
• Annotate genes

Sitka Spruce Mitochondrion Results

• Largest complete mitochondrial genome
  of a gymnosperm (5.5 Mbp)
• Multipartite genome structure
• Rosette-like assembly graph
• 26 introns in 13 genes
• 13 trans-spliced introns in 7 genes

Western Redcedar Methods

• Trim adapters with Trimadap and NxTrim
• Count k-mers with ntCard
• Estimate genome size GenomeScope
• Assemble PE and MP reads with ABySS 2.0
• Correct assembly errors
  with Chromium reads using Tigmint
• Scaffold with Chromium reads using ARCS
• Assess genome completeness using BUSCO

Western Redcedar Results

• 12.5 Gbp genome size estimated by flow cytometry
  (Hizume et al. 2001 https://doi.org/d89svf)
• 9.8 Gbp genome size estimated by GenomeScope
• 7.95 Gbp assembled in scaffolds 1 kbp or larger
• 2.31 Mbp scaffold N50
• 1.71 Mbp scaffold NG50 (with G=10 Gbp)
• Tigmint improved NG50 by 14% over ARCS alone
• BUSCO 60.4% of core single-copy genes present
  53.9% complete, 6.5% fragmented, 39.6% missing

Efficient Assembly
of Large Genomes

1. Introduction
2. ABySS 2.0
3. Tigmint
4. UniqTag
5. ORCA
6. Organellar genomes of white spruce
7. Mitochondrial genome of Sitka spruce
8. Genome assembly of western redcedar
9. Conclusion