Table 1.

Effect of word size and bubble size on assembly quality measured by Detonate and Transrate.

Assembly		RSEM_EVAL scorea	SUGIT transcripts		Good contigsd	% Good contigs
			CRBB hitsb	N refs with CRBBc
Word size	W15_B50	-25,925,250,958	9,089	8,300	13,242	82.42
	W20_B50	-19,380,072,750	55,894	33,773	114,829	93.23
	W25_B50	-19,421,340,895	57,372	34,013	128,286	94.07
	W30_B50	-19,496,141,905	59,888	34,706	131,210	94.39
	W35_B50	-19,281,907,606	67,973	37,144	140,335	94.99
	W40_B50	-19,215,617,161	72,865	38,402	147,726	95.37
	W45_B50	-19,097,783,732	76,624	39,741	154,954	95.71
	W50_B50	-18,927,399,593	80,304	40,781	161,660	96.05
	W55_B50	-18,835,828,725	84,991	42,022	168,938	96.43
	W60_B50	-18,936,543,261	86,758	42,152	172,140	96.69
	W64_B50	-18,759,903,834	91,486	43,405	178,809	96.96
Bubble size	W20_B50	-19,380,072,750	55,894	33,773	114,829	93.23
	W20_B150	-18,123,264,583	54,469	33,434	110,251	93.13
	W20_B250	-17,676,552,772	52,661	32,806	106,413	92.96
	W20_B350	-17,523,013,646	51,425	32,345	103,694	92.81
	W20_B450	-17,418,564,960	50,285	31,884	101,551	92.77
	W20_B550	-17,368,072,051	49,086	31,446	99,462	92.63
	W20_B650	-17,346,490,818	48,440	31,061	98,611	92.67
	W20_B1000	-17,274,641,924	47,491	30,905	97,653	92.55
	W20_B2000	-17,241,940,468	45,698	30,354	94,482	92.36
	W20_B3000	-17,208,740,562	45,491	30,241	92,987	92.17
	W20_B4000	-17,240,401,414	44,233	29,750	91,388	92.15
	W20_B5000	-17,250,943,232	43,935	29,550	90,434	92.18

^aThe higher the score, the better the assembly.

^bNumber of contigs in assembly with a Conditional Reciprocal Best BLAST (CRBB) hit.

^cNumber of sequences (out of 107,598 sequences in the SUGIT database) with a CRBB hit.

^dContig with a positive RSEM-EVAL impact score.