Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome

BMC Genomics

Table 2 Summary of GS FLX Long Paired End assemblies

	PE only	PE+SG	PE+SG+BE	S0022P24
Large contigs^a (> 500 bp)	310	289	286	14
Average contig size (bp)	2686	3058	3149	8885
N50 contig size^b (bp)	4160	4728	5635	32866
Contigs assembed into scaffolds^c	203	186	175	9^h
Total scaffolds	9	3	4	2
Large scaffolds^d (> 10 Kb)	6	3	4	2
Average large scaffold size (bp)	96257	299378	226679	112155
Largest scaffold size (bp)	227111	501016	538994	137857
N50 scaffold size^e (bp)	197327	361606	538994	137857
Total gaps^f	194	183	171	8
Maximum gap size (bp)	1,881	2,100	2,131	unknown
Minimum gap size (bp)	4	4	8	unknown
Pair distance average^g (bp)	2680	2776	2782	N/A
Pair distance deviation (bp)	670	694	696	N/A
Total bases covering region	958507	1002840	1000926	231017
Depth of coverage	~26×	~56×	~56×	~10.5×

Results for GS FLX Long Range Paired End (PE) assembly alone and when combined with the GS FLX shotgun (SG) data and BAC-end (BE) sequences. ^aContigs are defined as more than one read joined by overlapping sequence. Large contigs are greater than 500 bp. ^bThe N50 contig size is defined as the largest contig size at which half of the total size of the contigs is represented by contigs larger than the N50 value. ^cA scaffold is defined as two or more contigs associated by paired ends. ^dLarge scaffolds are those consisting of more than 10,000 bp among all contigs therein. ^eThe N50 scaffold size is defined as the largest scaffold size at which half of the total size of the scaffolds is represented by scaffolds larger than the N50 value. ^fGaps represent unsequenced regions between two contigs known to be adjacent due to associated paired ends. ^gAverage pair distance is the average distance between two sections of BAC DNA separated by linker sequence. ^hAssembly based on large contigs (> 500 bp) consisting of ≥3 reads each.

ISSN: 1471-2164