The transcript catalogue of the short-lived fish Nothobranchius furzeriprovides insights into age-dependent changes of mRNA levels

Table 2 Assembly metrics ^a

		First assembly ^a		Second assembly ^b
Method	TGICL	Newbler	PAVE	Iterative assembly procedure
Input datasets	Sanger, 454/Roche	Sanger, 454/Roche	Sanger, 454/Roche	PAVE contigs, Solexa/Illumina
Number of contigs (≥ 300 bp)	134,225	141,973	118,795	213,621
Total length of contigs (≥ 300 bp)	85.1 Mb	78.1 Mb	86.9 Mb	252.9 Mb
Average length of contigs	634 bp	549 bp	731 bp	1,183 bp
Median length of contigs	474 bp	434 bp	495 bp	676 bp
Maximum length of contigs	9,221 bp	7,841 bp	9,241 bp	64,116 bp
Number of large contigs (≥ 1 kb)	15,516	11,756	23,534	79,035
Total length of large contigs	24.9 Mb	19.1 Mb	38.3 Mb	183.0 Mb

^a ‘First assembly’ shows the results of three assembly programs that were tested using Sanger and 454/Roche data. PAVE produced the best assembly with respect to total length, number of contigs and average contig length. ^b ‘Second assembly’: Solexa/Illumina data were assembled onto a backbone of PAVE contigs using an iterative assembly procedure outlined in Methods.

ISSN: 1471-2164