|
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
