Question: Reconstruct original fragment from paired end reads
gravatar for tomaz
4.2 years ago by
tomaz10 wrote:


I would like to reconstruct my environemental 16S PCR fragments (slightly more than 300 bp) from my paired end reads (illumina, 250bp). I have good quality reads (more than 200 bp in length) from both ends of the original fragments and they should overlap well to reconstruct the ~300 bp originals. 

Is there a tool in galaxy that would do this job...that is, overlap the two paired ends to make/reconstruct one fragment. If not, what is the best tool available elsewhere to do the job?

I will greatly appreciate any commnets and suggestions!


assembly alignment galaxy • 1.1k views
ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by tomaz10
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool in the Tool Shed ( will do the job on a local or cloud Galaxy:

This is not on the public Main Galaxy instance - and should not be confused with the tools there that either merge the two paired ends into the same dataset or merges the sequence data end-to-end based on common sequence identifiers (or ordering of the input datasets).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
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