How to set the distance of paired reads for de novo assembly?

[NGS group]

Hi everyone,

I am using CLC bio to do the de novo assembly of bacterial genomes. I found that changing the setting of distance of paired reads during importing the raw data could significantly affect the quality of de novo assembly (i.e. the counts of contigs). But I have no idea how to optimize such setting, which is not explained in the user guide of CLC.

Is there anyone knows? Thank you very much!

-Victor

[mastal]

How to set the distance of paired reads for de novo assembly?

You should get an estimate of the insert size from the sequence provider or whoever produced the sequencing libraries.

[NGS group]

Can I estimate the insert size based on the data of Bioanalyzer?

[Wallysb01]

Can I estimate the insert size based on the data of Bioanalyzer?

Yes. You can also check the insert size after the fact when the reads are mapped back to your de novo genome.

[NGS group]

OK, thank you very much for your helps. I am going to have a try.