Near-optimal assembly for shotgun sequencing with noisy reads

BMC Bioinformatics

Table 2 Simulation results on the assembly of several real genomes using reads corrupted by substitution noise ((a) Prochlorococcus marinus (b) Helicobacter pylori (c) Methanococcus maripaludis (d) Mycoplasma agalactiae)withℓ_crit = max(ℓ_int,ℓ_tri), ${\tilde{ℓ}}_{crit} = max ({\tilde{ℓ}}_{int}, {\tilde{ℓ}}_{tri})$ and N_noiseless is the lower bound on number of reads in the noiseless case for 1 - ϵ = 95% confidence recovery

Index	Species	G	p	$\frac{N L}{G}$	L	${\tilde{l}}_{max}$	${\tilde{l}}_{crit}$	ℓ_crit	% match	Ncontig	$\frac{N}{N_{n o i s e l e s s}}$	$\frac{L}{ℓ_{crit}}$
1	a	1440371	1.5%	37.36 X	930	1817	803	770	100.00	1	1.57	1.21
2	a	1440371	1.5%	33.14 X	970	1817	803	770	99.95	1	1.67	1.26
3	a	1440371	1.5%	29.60 X	1000	1817	803	770	99.99	1	1.66	1.30
4	b	1589953	1.5%	40.82 X	2440	4183	2155	2122	100.00	1	1.30	1.15
5	b	1589953	1.5%	21.31 X	2752	4183	2155	2122	99.99	1	1.19	1.30
6	b	1589953	1.5%	20.66 X	2900	4183	2155	2122	99.99	1	1.35	1.37
7	c	1772693	1.5%	30.03 X	3950	5018	3234	3218	99.96	1	1.36	1.23
8	c	1772693	1.5%	21.96 X	4279	5018	3234	3218	99.97	1	1.33	1.33
9	c	1772693	1.5%	17.03 X	4700	5018	3234	3218	100.00	1	1.31	1.46
10	d	1006701	1.5%	35.23 X	6867	15836	10518	5494	99.05	1	1.72	1.25
11	d	1006701	1.5%	19.88 X	7500	15836	10518	5494	97.86	1	1.30	1.37
12	d	1006701	1.5%	17.69 X	9000	15836	10518	5494	98.10	1	1.68	1.64

ISSN: 1471-2105