Paired-end Sequencing

• 40 kbp Fosmid
• 200 kbp BAC
• 800 bp Illumina paired-end
• 6 kbp Illumina mate-pair

Large Molecule Sequencing

• PacBio
  • up to 100 kbp reads
• Oxford Nanopore
  • up to 500 kbp reads

New Technologies

• 10x Genomics Chromium Linked Reads
  • up to 200 kbp molecules
• BioNano Genomics Irys
  • up to 1000 kbp molecules

Long Read Assemblers

• Canu: PacBio or Nanopore
• Falcon: PacBio
• Miniasm: PacBio or Nanopore
• SPAdes: PacBio or Nanopore with Illumina

Polish

• Nanopolish for Nanopore
• Pbdagcon for PacBio
• Pilon for Illumina

Assemble Chromium

• Supernova
• ABySS for contigs, scaffolding is under way

Scaffold with Chromium

• Fragscaff (intended for an older technology)
• Architect
• BCGSC ARCS with LINKS

Scaffold with BioNano

• HybridScaffold

Sitka Spruce Mitochondrion

Aim

Assemble the Sitka spruce mitochondrion into a single scaffold* using 10x Chromium data.

* if it has a single chromosome

Method

• Align Sitka spruce reads to white spruce organelles
• Filter out mismapped nuclear reads (AS < 40)
• Identify 10x barcodes that contain at least one mitochondrial molecule
  • Four properly-paired mitochondrial reads
• Select all the reads of these mitochondrial barcodes
• Assemble with ABySS
• Scaffold with ARCS and LINKS
• Fill gaps with Sealer
• Annotate genes with MAKER
• Submit to NCBI GenBank

Links

ABySS | ARCS | Architect | Canu | Falcon | Fragscaff | HybridScaffold | LINKS | MAKER | Miniasm | Nanopolish | Pbdagcon | Pilon | Sealer | SPAdes | Supernova

Shaun Jackman

BC Cancer Agency Genome Sciences Centre
Vancouver, Canada
@sjackman | github.com/sjackman | sjackman.ca