Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

Table 5 Assembly statistics

Assembler	Sequencing	Strains	Insert size	Read length (bp)	Number of reads	Raw read coverage	Assembled bases (Mb)	Contig coverage	Contig N50
FuzzyPath	Illumina	CAST/Ei	200 bp	36	173 million	65×	76.03	80.0%	2,315
Velvet*	Illumina	CAST/Ei	200 bp	36	173 million	65×	58.09	61.15%	391
ABySS	Illumina	CAST/Ei	200 bp	36	173 million	65×	72.80	76.63%	1,022
FuzzyPath	Illumina	A/J	200 bp	36	112 million	42×	55.87	58.8%	959
Phusion	Capillary	A/J	3-5 kb	400-900	357,100	2.5×	81.2	85.5%	3,377
FuzzyPath	Hybrid	A/J^†	Hybrid^†	Hybrid^†	Hybrid^†	Hybrid^†	85.54	90.0%	5,793

*Version 0.4. We also tried the latest version 0.7, which had been much improved in terms of contig length, but ran out of memory on a computer with 192 Gb RAM. ^†Assembly incorporating the A/J Illumina reads and Celera capillary reads.

ISSN: 1474-760X