Table 1 Sequencing strategies (top) and assembly protocols (bottom) evaluated in the three case studies
NameRead TypeParameters for Read Simulation
LIB1Illumina PEDepth: 50 ×; read length: 100 bp; insert size: 180 ± 9 bp
LIB2Illumina MPDepth: 50 ×; read length: 100 bp; insert size: 8000 ± 400 bp
LIB3Illumina PEDepth: 50 ×; read length: 250 bp; insert size: 450 ± 23 bp
LIB4PacBio CLRDepth: 60 ×; read accuracy: 0.87 ± 0.03; read length: 11,500 ± 8000 bp
LIB5PacBio CLRDepth: 10 ×; read accuracy: 0.87 ± 0.03; read length: 11,500 ± 8000 bp
NameAssemblerSequencing strategies used for assembly
ILMN1ABYSSLIB1, LIB2 (Illumina-only)
ILMN2ALLPATHS-LG
ILMN3MaSuRCA
ILMN4SGA
ILMN5SOAPdenov2
ILMN6SPAdes
ILMN7Velvet
METAMetassembler
ILMN8DISCOVARLIB3 (Illumina-only)
PACB1Celera AssemblerLIB4 (PacBio-only)
PACB2Canu
PACB3FALCON
HYBR1SPAdesLIB1, LIB2, LIB5 (Hybrid)
HYBR2DBG2OLCaLIB1, 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.