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

BMC Genomics

Table 1 Change in reference agreement attributable to hybrid assembly methods

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%

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

ISSN: 1471-2164