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Old 08-30-2011, 05:31 AM   #1
narain
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Location: Washington DC

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Arrow SOAPdenovo for ABySS contigs

Dear All

I am using ABySS to generate contigs from human reads. I now want to make scaffolds from it. I used SSPACE but did not get as good result as wit E.coli reads. Or may be I have not yet explored fully to how to optimize use of SSPACE, though I did try changing its parameters a bit.

Can the scaffolder inbuilt in SOAPdenovo scaff be used to make scaffolds from contigs generated from ABySS ? Has anyone tried it ? What are the other option tools for scaffolding ?

Aby
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Old 08-30-2011, 09:44 PM   #2
jimmybee
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How about something like Phred/Phrap?
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Old 04-16-2012, 09:50 AM   #3
hylei
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i tried to de novo assembly the miseq PE 2X150 seq. Can anyone please suggest which assembler is better? Thanks.
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Old 04-16-2012, 10:31 AM   #4
aloliveira
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hylei,

There is no such thing as "better or worst assembler". Every one has your own advantages and disadvantages. SOAPdenovo, ABySS and Velvet are commonly used when we're dealing with short-reads databases. But there is a lot of new assemblers being developed (for example Ray). Perhaps you should read the papers and find out what is the best option for you.

Velvet:
http://genome.cshlp.org/content/18/5/821.short
http://www.plosone.org/article/info%...l.pone.0008407

ABySS:
http://genome.cshlp.org/content/19/6/1117

SOAPdenovo:
http://genome.cshlp.org/content/earl.../gr.097261.109

For a good review:
http://www.sciencedirect.com/science...88754310000492

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