how to use CLC bio software for assemly with SOLiD

noas · 12-07-2011, 04:03 AM

Hello all,
I am completely new commer to NGS technology and SOLiD platform.
I want to do de novo assembly of SOLiD data with the CLC bio software
clc_novo_assmble. apprently this software accepts fastq files for the assembly while I have .csfasta+ qual files. do I need to convert the csfasta+qual to fasq first? do I need to translate it from color space to nt space before doing the assembly?

Thanks for your help

colindaven · 12-07-2011, 07:07 AM

No, you don't need to convert to fastq if you're using the graphical CLC bio version 4.8+ or probably many earlier versions (I don t know what clc_novo_assmble is!).

In general, you definitely want to stay in colour space with Solid assemblies if at all possible.

noas · 12-07-2011, 08:38 AM

Thank you for your quick answer.

I will try to use the graphical interface as it is aparently more freindly...
I tried to use the command line for the novo assembly that is called clc_novo_assemble and it seems like it only accepts fastq files as input while I have csfasta+qual files

I would have liked to know if someone uses command line clc de novo assembly with color space data ...

NextGenSeq · 12-08-2011, 06:54 AM

Why are you using command line? You can import them in and start the assembly using the GUI interface.

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12-07-2011, 04:03 AM	#1
noas Junior Member Location: Israel Join Date: Dec 2011 Posts: 2	how to use CLC bio software for assemly with SOLiD Hello all, I am completely new commer to NGS technology and SOLiD platform. I want to do de novo assembly of SOLiD data with the CLC bio software clc_novo_assmble. apprently this software accepts fastq files for the assembly while I have .csfasta+ qual files. do I need to convert the csfasta+qual to fasq first? do I need to translate it from color space to nt space before doing the assembly? Thanks for your help

12-07-2011, 07:07 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 417	No, you don't need to convert to fastq if you're using the graphical CLC bio version 4.8+ or probably many earlier versions (I don t know what clc_novo_assmble is!). In general, you definitely want to stay in colour space with Solid assemblies if at all possible.

12-07-2011, 08:38 AM	#3
noas Junior Member Location: Israel Join Date: Dec 2011 Posts: 2	Thank you for your quick answer. I will try to use the graphical interface as it is aparently more freindly... I tried to use the command line for the novo assembly that is called clc_novo_assemble and it seems like it only accepts fastq files as input while I have csfasta+qual files I would have liked to know if someone uses command line clc de novo assembly with color space data ...

12-08-2011, 06:54 AM	#4
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	Why are you using command line? You can import them in and start the assembly using the GUI interface.