Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

BMC Bioinformatics

Table 3 Genome-specific mate-pair lengths used in SOAPdenovo assemblies

Organism	K-mer Size	t1 (bp)	t2 (bp)
Acinetobacter baumanii	35	165	276
	100	454	1708
Bacillus anthracis	35	157	451
	100	464	839
Bacteroides thetaiotamicron	35	159	297
	100	462	1759
Deinococcus radiodurans	35	145	745
	100	485	930
Mycobacterium tuberculosis	35	155	288
	100	491	824
Rickettsia prowazekii	35	170	288
	100	467	N/A
Staphylococcus aureus	35	154	436
	100	461	943
Vibrio parahaemolyticus	35	161	298
	100	440	N/A

'Tuned' mate-pair lengths used when performing SOAPdenovo assemblies. The values t1 and t2 refer to the best and second best mate-pair lengths respectively. These values are based on determination of 'ideal' mate-pair sizes for the 35 and 100-mer graphs (as described in Results).

ISSN: 1471-2105