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Image2 Input Questions

I am able to run IMAGE2 after creating read.placed.original and contigs.fa.original in the required format. Here are my questions: * Is it possible to supply multiple insert libraries to IMAGE? If yes, how? * What is the difference between "insert size" and "velvet inslen" in submit.iteration.log? * I am working with a bacterial genome. So I assume that all contigs will go into Supercontig1 in read.placed.original. Is that correct?

Please let me know if any question is unclear. Is there a IMAGE mailing list? I was not able to find one on the sourceforge project page. Thanks

-SS

assembly scaffolding
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written by Surya Saha Surya Saha

I'm not familiar with IMAGE (yet), but working with SSPACE, I find that working iteratively, starting with libraries with small insert sizes, and ending up with the longest, tend to give better results than running them all at once.

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written by Ketil Ketil

could you please let me know how to create the file read.placed.original and contigs.fa.original???

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written by HG HG

1 answer

Here is what I learned from the authors

  • Is it possible to supply multiple insert libraries to IMAGE? If yes, how? Ans: No
  • What is the difference between "insert size" and "velvet ins_len" in submit.iteration_.log? Ans: insert size is the mapping parameter used in ssaha or bwa. velvet ins_len is the insert size used in velvet.
  • I am working with a bacterial genome. So I assume that all contigs will go into Supercontig1 in read.placed.original. Is that correct? Ans: Yes

-SS

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written by Surya Saha Surya Saha

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