Bacterial WGS on Ion Torrent

[Ali Islam]

Hi There,..
We were running a bacterial WGS using Ion fragment library prep kit protocol.
After fragmentation of sample, we performed adaptor ligation and
did size selection of libraries using simple AGE gel exclusion of 200-400bp region from smears (due to unavailability of other size selection options)
We quantified libraries using Ion Universal Library Quantification Kit.

Picture of AGE gel is attached.
Quantification results were up to the mark giving individual libraries quantities above 100pm.

After equalization, we put our libraries on IonChef for Templating, and then on Ion S5 XL for sequencing.
Results gave median length of 50bp and after assembly a contiguous sequence of 500bp per sample.

Need troubleshooting on this case.

Looking forward to hearing from NGS experts.
Thanks in anticipations.

Best Regards.

[Hamid Ali]

was that the Ion Torrent™ Ion Xpress™ Plus Fragment Library Kit (Cat. No. 4471269) for preparing library or he Ion Plus Fragment Library Kit (Cat. No. 4471252) because the later involves physical fragmentation via sonication method .

[Ali Islam]

Surely the same as mentioned above. But we did enzymatic fragmentation by Ion Shear fragmentation kit because no physical fragmentation strategy was available.