Denovo assembly

[Thenna]

Hi, I am new to sequence assembly donot have knowledge on any software program. I am using CLC genome workbench for the denovo assembly and working on assembling bacterial genome that comes from Ion PGM.
1. I did assembling of bacterial data (300X coverage) using denovo assembly option in CLC and got around 90 contigs for 1.2Mbp genome. How to reduce number of contigs when reference genome is not available. Also I tried making contigs from the contigs obtained from the first assembly. But No significant improvement.
2. Same data I assembled using reference. It gave me 100% match.

I think I am missing something during denovo assembly. I use default assembly parameters suggested by the CLC, also I trim the raw sequences for the adopter removal. Any suggestions highly appreciated. Also please suggest me if any online tool available for the assembly which can be used by any biologist who doesnot have software knowledge..

Thanks
Thenna

[krobison]

If you have a reference available, then mapping your contigs back to it might give some insight into the nature of the breaks. Some may simply not be crossable using Ion Torrent technology -- large repeats in particular. Some may be missed overlaps; you may be able to identify errors that prevented joining, but since CLC is a black box there probably isn't much more debugging that can be done with that. You can play with the parameters, but I don't have any experience with CLC to suggest which to play with.

[GenoMax]

Consider contacting CLCBio tech support. They are generally very responsive. That may also be the quickest way to get suggestions on different parameters to try for assembly.