GAML: genome assembly by maximum likelihood

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

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

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.

ISSN: 1748-7188