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Old 12-07-2011, 04:03 AM   #1
noas
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Location: Israel

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Default 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
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Old 12-07-2011, 07:07 AM   #2
colindaven
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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.
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Old 12-07-2011, 08:38 AM   #3
noas
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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 ...
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Old 12-08-2011, 06:54 AM   #4
NextGenSeq
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Why are you using command line? You can import them in and start the assembly using the GUI interface.
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