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Table 1 Alignment of contigs from different data sets to the AGPv2 reference genome using BLAST. To be classified as aligned, contigs must match the reference with ≥95% identity

From: Linked read technology for assembling large complex and polyploid genomes

No. Alignments No. Contigs (%) from
LR Contigs Trimmed LR Contigs MAGIs Sim 1a Sim 2b Sim 3c ABySS
1 (Unique) 222,531 (95.0) 222,245 (95.1) 109,665 (96.1) 256,255 (98.7) 262,727 (98.8) 257,049 (98.7) 4,614,334 (42.9)
2 2145 (0.9) 2194 (0.9) 1347 (1.2) 1985 (0.8) 2014 (0.8) 1971 (0.8) 1,520,610 (14.1)
>  2 629 (0.3) 535 (0.2) 138 (0.1) 568 (0.2) 488 (0.2) 716 (0.3) 4,268,325 (39.7)
0 8848 (3.8) 8931 (3.8) 3024 (2.6) 762 (0.3) 719 (0.3) 790 (0.3) 350,313 (3.26)
Total 234,153 233,905 114,173 259,570 265,968 260,526 10,753,582
  1. aSimulation 1: 50 kb molecule length and 400 M reads
  2. bSimulation 2: 80 kb molecule length and 400 M reads
  3. cSimulation 3: 50 kb molecule length and 800 M reads