Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes

Table 2 Impact of sequencing depth on subtractive assembly for S. thermophilus LMD-9

Sequencing depth		Base coverage^b (%)	Extracted reads^c (%)	Assembled genome^d (%)
S1^a	S4	Base coverage^b (%)	Extracted reads^c (%)	Assembled genome^d (%)
4×	1×	82.15	86.69	31.72
8×	2×	86.96	88.93	67.31
12×	3×	90.58	93.15	83.72
16×	4×	92.96	95.53	90.92
20×	5×	94.79	96.91	93.82

^aThe community structures of S1 and S4 are the same as in simulation 1 (group 1 in Table 1)
^bExpected percentage of bases with ≥ 2 times sequencing coverage in S1 than in S4
^cPercentage of reads extracted from the simulated S. thermophilus genome in S1
^dFraction of the genome assembled using the extracted reads by our subtractive assembly approach

ISSN: 1474-760X