Table 1 Summary statistics among seven highest performing assembly strategies
From: Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
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 |