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Old 07-22-2013, 08:03 AM   #1
hi-koike
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Location: Japan

Join Date: Jul 2013
Posts: 13
Question overlapping in PE library sequencing

Hello,

I'd like to do de novo assembling of a fungal genome(~20 Mbp).
I will use Miseq data for the assembling.

I found some programs can handle overlapping sequence of the two
paired end reads such as ALLPATHS-LG and FLASH.

I am wondering how long of the fragment length for paired read is appropriate for the version2 of Miseq.
Now the read length of the Miseq v2 is 250 bp, paired reads from fragments of size ~400 bp or more would be overlapping. On the other hand, the bases in the terminus might be low quality and can not be used, right?

I guess longer fragments would be effective in getting information from the same number of reads, while it would be meaningless if the reads would be too short to overlap due to their low quality.
Has anyone try to input overlapping fragment library from the fragments of
more than 400 bp for any de novo assembling ?

Many thanks,
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