Shaun Jackman

Thesis Committee

Timeline

• Previous meeting 2015-07-27
• Fourth committee meeting 2018-03-14
• Start writing early 2018
• Submit thesis and defend late 2018
• Graduate spring 2019

Conferences

• Three talks and four posters
• ISMB 2016 BOSC talk and poster
  Linuxbrew and Homebrew for Cross-platform Package Management
• ISMB 2016 HiTSeq poster
  Organellar Genomes of White spruce (Picea glauca): Assembly and annotation
• PAG 2017 talk and AGBT 2017 poster
  Organellar Genomes of Sitka Spruce (Picea sitchensis): Assembly and Annotation
• ISMB 2017 talk and poster
  Tigmint: Correct Misassemblies Using Linked Reads From Large Molecules

Teaching Assistant

UBC Master of Data Science

• 2016 DSCI 522 Data Science Workflows
• 2017 DSCI 531 Data Visualization I

Papers

• Assembly of the complete Sitka spruce chloroplast genome using 10X Genomics’ GemCode sequencing data L Coombe, RL Warren, SD Jackman, C Yang, BP Vandervalk, RA Moore, …
  PloS one 2016
• Spaced seed data structures for de novo assembly
  I Birol, J Chu, H Mohamadi, SD Jackman, K Raghavan, BP Vandervalk, …
  International journal of genomics 2015
• Konnector v2.0: pseudo-long reads from paired-end sequencing data
  BP Vandervalk, C Yang, Z Xue, K Raghavan, J Chu, H Mohamadi, SD Jackman,…
  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
• Improved white spruce (Picea glauca) genome…
  RL Warren, CI Keeling, MMS Yuen, A Raymond, GA Taylor, …
  The Plant Journal 2015

Papers

• Three first-author (or joint) papers since 2015
• Collaborated on 29 papers since 2009
• 25 papers with at least 10 citations
• Two first-author manuscripts in preparation

Manuscripts

• ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research SD Jackman^*, T Mozgacheva^*, B O’Huiginn, L Bailey, I Birol, SJM Jones
• Tigmint: Correct Assembly Errors Using Linked Reads From Large Molecules SD Jackman, J Chu, RL Warren, BP Vandervalk, L Coombe, S Yeo, …

Thesis Outline

Methods

1. ABySS 2.0: resource-efficient assembly of large genomes
2. Tigmint: Correcting misassemblies using linked reads
3. UniqTag: Content-derived unique and stable identifiers

Genomes

1. Organellar genomes of white spruce (Picea glauca)
   using paired-end and mate-pair reads
2. Organellar genomes of Sitka spruce (Picea sitchensis)
   using linked reads and Nanopore reads
3. Genome assembly of western redcedar (Thuja plicata)
   using paired-end, mate-pair, and linked reads

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 Plastid

• Assembled by Rene Warren and Lauren Coombe
  using linked reads
• Annotated genes (mRNA, rRNA, tRNA)
• Submitted annotated genomes to GenBank
• Published paper in PLOS ONE (2016)

Sitka Spruce Mitochondrion

• 10x Genomics Chromium sequencing
• > 50x mitochondrial coverage in one lane
• 11 lanes of Oxford Nanopore Sequencing
• 3x nuclear coverage
• 14x mitochondrial coverage
• Assemble Nanopore reads
  with Canu and Unicycler
• Scaffold and polish with linked reads

Sitka Spruce Mitochondrion

• Complete the genome assembly
• Determine chromosomal structure
• Annotate the genome
• Submit the genome to GenBank
• Write the manuscript

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)
• Presenting a talk at RECOMB-Seq 2018

Tigmint

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
• Presenting a talk and poster at RECOMB-Seq 2018

Western Redcedar (Thuja plicata)

Method

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

Results

• Scaffold NG50 of 1.2 Mbp
• BUSCO 54% complete, 7% fragmented

Thesis Outline

Methods

1. ABySS 2.0: resource-efficient assembly of large genomes
2. Tigmint: Correcting misassemblies using linked reads
3. UniqTag: Content-derived unique and stable identifiers

Genomes

1. Organellar genomes of white spruce (Picea glauca)
   using paired-end and mate-pair reads
2. Organellar genomes of Sitka spruce (Picea sitchensis)
   using linked reads and Nanopore reads
3. Genome assembly of western redcedar (Thuja plicata)
   using paired-end, mate-pair, and linked reads