Table 1

Summary statistics among seven highest performing assembly strategies
Assembly strategies Percent reference coverage (bp) Percent reference genes assembled to >200 bp Percent reference genes assembled to ≥80% Percent chimeric Redundancy
Oases filter1-cap3-blast 26.50% 45.70% 10.52% 0.96% 2.42
Oases filter1&3-cap3-blast 27.67% 45.65% 11.73% 1.11% 2.41
SOAPdenovo-Trans k=21-cap3-blast 32.75% 45.62% 16.20% 2.21% 1.78
SOAPdenovo-Trans contigs cap3-blast 30.64% 46.62% 14.34% 1.06% 2.19
Trans-ABySS MK-cap3-blast 28.34% 42.93% 13.01% 1.39% 2.16
Trinity blast 26.22% 47.06% 9.58% 1.69% 3.11
Trinity pickH-cap-blast 23.19% 45.38% 8.35% 0.92% 1.89

The best score for each column, measured as highest in reference coverage and lowest in chimera rate and redundancy, is in bold.

Yang and Smith

Yang and Smith BMC Genomics 2013 14:328   doi:10.1186/1471-2164-14-328

Open Data