Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

Table 2 Description of assemblies, Illumina reads and performance of IMAGE

	Statistics of draft assembly			Illumina reads used			IMAGE performance
Organisms	Read type	Size (Mb)	N50^a(kb)	Read length	Coverage^b	Insert size^c	Total gaps^d	Gaps closed
Salmonella enterica 1	454	4	117	54	295	225	73	49 (68%)
Salmonella enterica 2	Illumina	4	87	54	274	220	233	194 (83%)
Clostridium difficile	454	4	76.5	54	331	249	118	55 (47%)
Bordetella bronchiseptica	454	5	5	54	420	321	918	397 (43%)
Plasmodium berghei ^e	Cap+454+Illumina	18.5	189	76	140	130	156	71 (46%)
Leishmania donovani	454	30	10	76	83	176	3,826	1,768 (46%)
Echinococcus multilocularis	Cap+454	107	108	75	126	310	1,676	895 (53%)
Schistosoma mansoni	Cap	307	24	108	30	219	25,214	13,771 (55%)

^aThe minimum contig length cutoff to include contigs in a given assembly to have 50% of total assembled sequence. ^bEstimated coverage is calculated as Length of Illumina read × Number of reads/Assembled genome size. ^cInsert size is defined as the averaged physical distance between two sequenced fragments that were unambiguously aligned against the contig sequence of the initial assembly. ^dGap is defined as the region between contigs within a scaffold that has no sequence information. ^eThe core set of Plasmodium berghei contigs that were aligned to the closely related reference sequence of Plasmodium chabaudi. Cap, capillary reads.

ISSN: 1474-760X