Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

BMC Genomics

Table 2 Statistics of initial assembly

	AFSFASSS	AFSF	ASSS	AF	AS	SF	SS
Trinity
No. of contigs	227,879	110,162	198,382	69,721	133,556	76,474	126,848
Total Bases	217,485,766	89,132,635	184,623,552	3,9925,904	115,757,220	55,932,501	100,283,444
No. of contigs (> = 1 kbp)	69,402	28,016	58,759	6,817	36,825	16,409	30,694
Total Bases (in contigs > = 1 kbp)	135,112,080	47,002,017	112,433,788	9,818,210	65,495,871	25,146,108	50,760,639
Max contig length	12,488	7,710	10,506	5,723	11,199	5,670	5,294
Mean contig length	954	809	930	572	866	731	790
N50	1,370	1,060	1,323	600	1,165	903	1,015
No. of contigs in N50	46,815	25,597	41,204	20,241	29,723	19,351	30,035
ABySS
No. of contigs	571,835	258,087	478,056	157,039	334,220	158,856	279,549
Total Bases	35,941,1943	152,450,028	296,430,486	88,785,112	202,564,854	90,257,267	165,879,838
No. of contigs (> = 1 kbp)	66,393	22,844	52,783	11276	33,779	11,757	25,615
Total Bases (in contigs > = 1 kbp)	88,342,878	29,539,332	69,895,282	14,500,455	44,327,763	14,876,118	33,225,449
Max contig length	8,216	4,077	5,694	5,031	6,687	4,725	4,804
Mean contig length	628	590	620	565	606	568	593
N50	686	634	674	597	653	604	637
No. of contigs in N50	178,083	82,822	149,467	51,187	105,491	51,861	89,188

ISSN: 1471-2164