Table 2 Performance of all experimental designs evaluated in case study II
Nuclear:Mitochondrial Genome RatioPerformance of Strategiesa
Complete, Single Contig Assembly of the Mitochondrial GenomeAssembled Fraction of Mitochondrial Genome ≥ 99%20% ≤ Assembled Fraction of Mitochondrial Genome < 99%Assembled Fraction of Mitochondrial Genome < 20%
1:50 (low mitochondrial content)ILMN1, ILMN6, ILMN8, PACB2, HYBR1, HYBR2ILMN7ILMN2, ILMN4, ILMN5, PACB1, PACB3ILMN3
1:200 (high mitochondrial content)PACB2, HYBR1, HYBR2ILMN6, ILMN7ILMN1, ILMN8, PACB1, PACB3ILMN2, ILMN3, ILMN4, ILMN5
  • a The de novo assembly generated by each strategy was compared against the reference mitochondrial genome of S. cerevisiae using both QUAST and BLASTN. Unless a single contig was found to represent the complete mitochondrial genome, the assembled fraction of mitochondrial genome was determined based on the number of “missing reference bases” reported by QUAST, and further confirmed by the BLASTN result.