sjackman / tigmint-paper

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

Tigmint: Correct Misassemblies Using Linked Reads From Large Molecules

• Paper
• Poster
• Slides HTML · PDF · Markdown
• Software on GitHub and its web page

tigmint-paper's Issues

Revisions

• Use spanning molecules @lcoombe
• Report time and memory usage @sjackman
• Explore parameter space, optimize parameters, demonstrate parameter sensitivity @lcoombe
• Describe the parameter of maximum distance between two reads in a molecule (50 kbp), demonstrate parameter sensitivity @lcoombe
• Compare other assemblers @sjackman
  • DISCOVARdenovo + BESST
  • Falcon assembly of HG004 Pacbio
  • Canu assembly of N12878 Nanopore
• Add percent reduction in breakpoints to both tables @sjackman
• Use QUAST 5 http://cab.spbu.ru/software/quast-lg/ @sjackman
• Analyze a synthetic data set @sjackman
  • Create synthetic paired-end and mate-pair reads with wgsim
  • Assemble the synthetic data set with ABySS
  • Create synthetic linked reads using LRsim
  • Run Tigmint and ARCS
  • Quantify precision and recall
• Optimize LINKS parameters -a -l -z
• Add tick mark labels to the y-axis of figure 2 @sjackman

Plan