Insert size and contig length

[morning latte]

Hello all,

I am wondering if there is any correlation between sequencing library insert size length and assembled contig length. I thought the use of long insert size will likely generate longer contig length? So I should ask a sequencing facility to use long insert size available (about 600 bp) for my metagenomes? Currently, I am using Illumina HiSeq platform and the sequencing facility is using TruSeq kit for library prep. Any advice or idea would be appreciated.

[Brian Bushnell]

There is not necessarily a direct correlation between insert size and contig length with a pure DBG assembler, though I would expect longer inserts to possibly give more uniform coverage.

Longer insert size will give you better scaffolding, though. And gaps captured within scaffolds can potentially be filled, which increases contig length. So, unless you are merging reads by overlap, I suggest the longest insert size available for a fragment library.

[morning latte]

Thank you Brian for the suggestion!