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Old 11-04-2013, 08:36 PM   #1
Bgansw
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Location: Sydney, Australia

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Default Illumina nextra sequencing

Hello,

I'm trying to assemble my illumina sequenced- cyanobacterial genome.. using soapdenovo and velvet, but I'm getting extremely low N50's like less than a 1000. I've never faced such a problem with any of my previous sample genomes.

Please help!

bgansw
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Old 11-05-2013, 06:36 AM   #2
krobison
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What have you done to QC your sequences? Are you trimming them? If you map your reads back to the assembly, what insert size to you get? What range of k are you trying?

Nextera can generate very short insert libraries if things go wrong -- and if you get those, your reads will be badly contaminated with sequencing adapters.
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Old 11-05-2013, 08:08 AM   #3
mcnelson.phd
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You're reads were most likely NOT adapter trimmed. This has caused a number of people problems with assembly of Nextera data.

Do that before assembling and you should get normal looking N50 values.
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