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Table 3 Statistics on inversions, translocations and relocations in 20 scaffoldings of the human genome

From: L_RNA_scaffolder: scaffolding genomes with transcripts

Software Library Connections Consistent Inversion Translocation Relocation
   Total Correctable*
SOAPdenovo 2 kb 6 4 0 0 2 2
5 kb 4,320 4,196 0 0 124 124
10 kb 5,456 5,394 0 0 62 62
35 kb 15,765 14,930 0 82 753 744
SOPRA 2 kb 3,717 3,701 0 0 16 8
5 kb 11,786 11,665 0 0 121 104
10 kb 268 236 0 0 32 32
35 kb unfinished, cause unclear
Opera 2 kb 2,917 2,886 0 0 31 7
5 kb 11,095 10,968 0 0 127 101
10 kb 29 25 0 0 4 0
35 kb 23,149 22,058 0 224 872 829
MIP scaffolder 2 kb 129 84 0 1 44 43
5 kb 537 177 0 3 357 355
10 kb 12,626 12,452 0 3 171 171
35 kb 13,297 9,937 1 2,232 1,137 1,019
SSPACE 2 kb 14 11 0 0 3 3
5 kb 7,871 7,717 0 3 154 154
10 kb 7,616 7,532 0 0 84 84
35 kb 21,388 20,473 1 5 912 907
L_RNA_scaffolder   11,579 9,839 3 625 1,123 1,022
  1. Column headers are defined in the main text. *: if the interval between two contigs is smaller than MIL in the reference genome but they are joined together in the predicted assembly, this relocation is considered correct.