Graphical Fragment Assembly GFA 2.0

Shaun Jackman @sjackman

2017-01-18

https://sjackman.ca/gfa2-slides

Shaun Jackman

Common file format

• Interoperable modular tools
• Deduplication of effort
• Data visualization

Alignment

• Alignment and variant calling is a pipeline of two stages
• Alignment reads FASTQ produces SAM/BAM
• Variant calling reads SAM/BAM produces VCF

Benefits

Things we take for granted

• Mix and match aligners and variant callers
• Support tools (samtools) shared by everyone
• Visualization tools (IGV) shared by everyone
• Troubleshooting intermediate stages
• All possible because of SAM/BAM

Assembly

• Assembly is a pipeline
  Overlap, Layout, Consensus
• Common input file format (FASTQ)
• Common output file format (FASTA)
• No common intermediate file format

Deduplication of effort

• Developing a new variant caller doesn't require developing a new aligner
• Developing a new assembler shouldn't require developing a new read overlap tool

GFA 1

• Started as a blog post by Heng Li
• Sequence overlap graph
• Vertices (segments) are contigs
• Edges (links) are their overlaps
• Tab separated format
• Extensible (optional tagged fields)

Implementations

• ABySS
• Bandage
• bcalm2
• bfgraph
• Canu
• fermi mag2gfa
• gfakluge
• gfalint
• gfatools
• lmrodriguezr/gfa
• McCortex
• miniasm
• RGFA
• vg
• TwoPaCo

Limitations

• Intended for
  • Short read assembly
  • Contig overlap graph (not reads)
• CIGAR unwieldy for long read alignment
• Links represent only dove-tail overlaps

GFA 2

• Short and long read assembly
• Read overlap graph or contig overlap graph
• Arbitrary alignments (not just dovetail)
  • Correcting reads
  • Identifying repeats
• CIGAR or compact trace alignments
• Gap edges and paths for scaffolding

Exciting Possibilities

• Mixing components of assembly pipelines
• Visualization of intermediate results
  aids troubleshooting
• Align reads to a pan-genome
• Graph-aware gene annotation
• Innovation in modular assembly tools
  • Identify heterozygous contigs
  • Identify misassembled contigs
• Modular scaffolding tools
  • One tool produces gap edges
  • Another tool creates scaffolds

xkcd: Standards