Genome sequencing of bacteria: sequencing, de novoassembly and rapid analysis using open source tools

BMC Genomics

Table 1 Reference mapping results of type strain Alcanivorax borkumensis SK2 using pyrosequencing reads and comparison with de novo assembly (MIRA3)

SOFTWARE	Total bps covered by mapping/Length of missing fragments	Disagreements	Number of bps
MOSAIK	3 099 937
	20 206
		Ns	1535
		Tranversion/Transitions	2
		Insertions	10 225
		Deletions	7 733
NEWBLER	3 104 799
	15 344
		Ns	1 544
		Tranversion/Transitions	0
		Insertions	11 493
		Deletion	10 346
MIRA3	3 119 125
	1 018
		Ns	905
		Tranversion/Transitions	2
		Insertions	1 867
		Deletions	5 187
de novo	3 079 251
	40 892
		Ns	323
		Tranversion/Transitions	9 814
		Insertions	1 491
		Deletions	1 590

The difference between NC_008260 (3,120,143 bps) and the number of nucleotides covered corresponds to the total length of the genome not mapped. Disagreements are indicated as conflicting positions in the consensus sequence between reference genome and mapped reads. Ns – number of fully ambiguous nucleotides within mapped regions.

ISSN: 1471-2164