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Table 3 Improving existing assemblies of the human chromosome 14 by GAML

From: GAML: genome assembly by maximum likelihood

Assembler Number of scaffolds Longest scaffold (kb) Longest scaffold corr. (kb) N50 (kb) Err. N50 corr. (kb) LAP
Human chromosome 14, starting from Velvet assembly
 Before 1,081 4,628 263 1,190 9,156 27 −138.765779
 After 1,634 1,046 265 347 8,049 27 −138.632657
 REAPR 17,727 153 81 36 4,607 14 −162.869192
Human chromosome 14, starting from ALLPATHS assembly
 Before 129 81,640 14,918 81,640 34 7,652 −111.288806
 After 139 81,640 14,918 81,640 33 7,652 −111.287938
 REAPR 858 977 146 190 4,230 17 −168.024865
  1. In both experiments, we use read sets H1, H2, and H3 and compare the original assembly computed by another tool with the assembly found by GAML.