Denovo assembly

Thenna · 05-05-2013, 12:42 AM

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 · 05-06-2013, 06:38 AM

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 · 05-06-2013, 07:09 AM

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Anyone used Allpath-LG for denovo assembly?	ffish	Bioinformatics	12	07-21-2015 06:28 AM
question about denovo assembly	kenietz	Bioinformatics	26	05-13-2013 06:12 PM
Denovo assembly problem	huma Asif	Illumina/Solexa	1	03-27-2013 10:20 PM
parameters for Denovo assembly	nareshmvr	Illumina/Solexa	10	03-01-2013 11:12 AM
denovo assembly	nagaraj	Bioinformatics	5	07-11-2012 07:13 AM

05-05-2013, 12:42 AM	#1
Thenna Junior Member Location: Saudi Join Date: May 2013 Posts: 2	Denovo assembly 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

05-06-2013, 06:38 AM	#2
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	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.

05-06-2013, 07:09 AM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	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.