Table 1. Assembly evaluation metrics and results.

The W303 strain assembly in each step of IMAP, including the final one, was validated using evaluation metrics such as N50, the length of the shortest contig (MIN), the length of the longest contig (MAX), and total length. We also calculated the fraction of mapped reads and the portion of read pairs that were properly mapped.

Dataset (W303)		MIN (bp)	MAX (bp)	N50 (bp)	Total length (bp)	Mapped reads (%)	Proper pairs (%)
De novo assembly	SPAdes	80	515,973	187,035	13,901,101	99.40	96.24
	MaSurCa	300	784,921	273,283	11,838,299	82.86	97.88
	SOAPdenovo2	200	61,911	13,286	11,749,637	50.60	88.48
RACA assembly	RACA-SPAdes	80	1,058,428	716,084	13,905,771	99.40	96.24
	RACA-MaSurCa	300	1,436,612	706,991	11,842,202	82.86	97.88
	RACA-SOAPdenovo2	200	1,076,849	69,631	11,772,637	50.60	88.49
Meta assembly	Meta	80	1,448,740	702,641	13,773,679	98.56	96.19
Final assembly	Corrected assembly	80	1,450,556	705,629	13,847,490	98.57	97.10
PacBio	PacBio	3,688	1,575,129	929,095	12,433,409	99.15	98.73