Table 1. Sequencing strategies (top) and assembly protocols (bottom) evaluated in the three case studies.
| Name | Read Type | Parameters for Read Simulation |
|---|---|---|
| LIB1 | Illumina PE | Depth: 50 ×; read length: 100 bp; insert size: 180 ± 9 bp |
| LIB2 | Illumina MP | Depth: 50 ×; read length: 100 bp; insert size: 8000 ± 400 bp |
| LIB3 | Illumina PE | Depth: 50 ×; read length: 250 bp; insert size: 450 ± 23 bp |
| LIB4 | PacBio CLR | Depth: 60 ×; read accuracy: 0.87 ± 0.03; read length: 11,500 ± 8000 bp |
| LIB5 | PacBio CLR | Depth: 10 ×; read accuracy: 0.87 ± 0.03; read length: 11,500 ± 8000 bp |
| Name | Assembler | Sequencing strategies used for assembly |
| ILMN1 | ABYSS | LIB1, LIB2 (Illumina-only) |
| ILMN2 | ALLPATHS-LG | |
| ILMN3 | MaSuRCA | |
| ILMN4 | SGA | |
| ILMN5 | SOAPdenov2 | |
| ILMN6 | SPAdes | |
| ILMN7 | Velvet | |
| META | Metassembler | |
| ILMN8 | DISCOVAR | LIB3 (Illumina-only) |
| PACB1 | Celera Assembler | LIB4 (PacBio-only) |
| PACB2 | Canu | |
| PACB3 | FALCON | |
| HYBR1 | SPAdes | LIB1, LIB2, LIB5 (Hybrid) |
| HYBR2 | DBG2OLCa | LIB1, LIB5 (Hybrid) |
PE, paired-end; MP, mate pair; PacBio, Pacific Biosciences; CLR, continuous long-read.
a
SparseAssembler (Ye et al. 2012) was used to assemble LIB1 into contigs, which in turn were then used as input for DBG2OLC.