Mate pair and pair end

Jayakumar S · 05-06-2014, 03:16 AM

Hi,
Please help me to understand the utility of pair end and mate pair sequences in the case of livestock genome.
Also, I am not clear how the pair end and mate pair sequencing will affect the genome coverage?.
What should be the optimum insert size to be followed in livestock genome, if mate-pair libraries has to be created and used for the NGS?.
Which one is good, pair end or mate pair sequences to have the improved contig order?.

Thanks,
Jayakumar S

nucacidhunter · 05-06-2014, 05:48 AM

In paired-end sequencing fragment libraries are sequenced from termini of insert. The reads not only provide coverage but also provides distance information which can be useful in many applications such as de novo assembly and identifying structural variation. In Illumina systems cost per base or read for 2nd reads is less than single end read. Contigs from short reads cannot be assembled in repeat regions and collapse. In these cases mate pair libraries larger than repeat region size are particularly useful for orienting and ordering contigs relative to each other. Mate pair libraries usually are constructed by circularising long fragments (2-20 kb), shearing and capturing the termini junction followed by library prep and paired-end sequencing.

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05-06-2014, 03:16 AM	#1
Jayakumar S Member Location: India Join Date: Sep 2013 Posts: 34	Mate pair and pair end Hi, Please help me to understand the utility of pair end and mate pair sequences in the case of livestock genome. Also, I am not clear how the pair end and mate pair sequencing will affect the genome coverage?. What should be the optimum insert size to be followed in livestock genome, if mate-pair libraries has to be created and used for the NGS?. Which one is good, pair end or mate pair sequences to have the improved contig order?. Thanks, Jayakumar S

05-06-2014, 05:48 AM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	In paired-end sequencing fragment libraries are sequenced from termini of insert. The reads not only provide coverage but also provides distance information which can be useful in many applications such as de novo assembly and identifying structural variation. In Illumina systems cost per base or read for 2nd reads is less than single end read. Contigs from short reads cannot be assembled in repeat regions and collapse. In these cases mate pair libraries larger than repeat region size are particularly useful for orienting and ordering contigs relative to each other. Mate pair libraries usually are constructed by circularising long fragments (2-20 kb), shearing and capturing the termini junction followed by library prep and paired-end sequencing.