Skip to main content

Table 1 Change in reference agreement attributable to hybrid assembly methods

From: Hybrid assembly with long and short reads improves discovery of gene family expansions

Source Metric ALLPATHS PBJelly Alpaca
  Agreement    
Nucmer Alignment N50 20,539 +86% +99%
ATAC Alignment N50 174,306 +12% +27%
Quast NGA50 86,432 0% +30%
  Disagreement    
Quast Misassemblies 3784 +50% −17%
Quast Local misassemblies 9444 −21% −43%
Quast Misassembled contigs 1423 +17% −13%
  1. The rice Nipponbare genome was assembled with ALLPATHS and then re-assembled with the PBJelly and Alpaca hybrid methods. All assemblies were compared to the independently derived reference and reference agreement was measured relative to the ALLPATHS level. Top: the sizes of alignments to the reference characterized by N50. Nucmer alignments are bounded by contigs while ATAC “M c” alignments can span intra-scaffold gaps. Quast NGA adjusted N50 after breaking at mis-assemblies. Bottom: Quast uses Nucmer alignments to infer global and local mis-assemblies, where the former involve spans or transpositions of 1Kbp or larger