MiSeq Paired End Reads for Draft Assembly

[cktheory]

Hi Everyone,
I am trying to de novo assemble a draft bacterial genome with a single chromosome from another persons data. The insert size of the sequenced segments average to 580bp and the read length for the R1 and R2 files is 301. After filtering there is not enough overlap to merge the paired reads. Is there a way to still use this data to assemble a draft genome that can be annotated?

[Brian Bushnell]

Filtering does not change the read length. If the insert size is 580, then actually there is enough overlap to merge them - try BBMerge.

You don't need to merge them, though. You can just adapter-trim and then assemble with Spades. Merging and error-correction may give you a better assembly, but neither is required.