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Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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Is there an option for Ray to output reads not used in the assembly? Is this in the AMOS file? #65

Open sebhtml opened 12 years ago

sebhtml commented 12 years ago

Is there an option for Ray to output reads not used in the assembly? Is this in the AMOS file?

Reported-by: Keith Robison

mscook commented 12 years ago

Hi Seb,

I was interested using the protocol outlined in:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031002

I was having no such luck with the Ray amos file. I contacted the author and this was his response:

"Ray natively produce the afg file, however it is not complete. In particular it lacks all the "first" part in which reads are described. Without this information the bank cannot be constructed. If you have more than one library things get really messy!!! In order to "complete" the afg file for PLOSone paper I used the afg file from velvet. Ray is missing only the description part so it is not a problem to copy it."

I assume this relates to the issue above.

Regards

Mitch

sebhtml commented 12 years ago

Hello,

I am able to create a bank with AMOS from a Ray AMOS file.

The implementation is based on the specification:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Message_Types

Maybe the protocol uses optional information in the AMOS message protocol.

[boiseb01@ls30 RayKmerSearchDevel]$ bank-transact -b MyBank -c -m TestX/AMOS.afg START DATE: Tue Jun 26 08:32:41 2012 Bank is: MyBank 0% 100% AFG .................................................. Messages read: 20008 Objects added: 20008 Objects deleted: 0 Objects replaced: 0 END DATE: Tue Jun 26 08:32:42 2012

Mitchell J Stanton-Cook a écrit :

Hi Seb,

I was interested using the protocol outlined in:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031002

I was having no such luck with the Ray amos file. I contacted the author and this was his response:

"Ray natively produce the afg file, however it is not complete. In particular it lacks all the "first" part in which reads are described. Without this information the bank cannot be constructed. If you have more than one library things get really messy!!! In order to "complete" the afg file for PLOSone paper I used the afg file from velvet. Ray is missing only the description part so it is not a problem to copy it."

I assume this relates to the issue above.

Regards

Mitch

Reply to this email directly or view it on GitHub: https://github.com/sebhtml/ray/issues/65#issuecomment-6564621

sebhtml commented 11 years ago

Reported-by: Lionel Frangeul lfrangeu@pasteur.fr

sebhtml commented 11 years ago

@mscook

"Ray natively produce the afg file, however it is not complete. In particular it lacks all the "first" part in which reads are described. Without this information the bank cannot be constructed. If you have more than one library things get really messy!!! In order to "complete" the afg file for PLOSone paper I used the afg file from velvet. Ray is missing only the description part so it is not a problem to copy it."

I remember using Ray's afg file with this command:

bank-transact -m data.afg -b data.bnk -c

Please open a separate issue if you feel like this should be fixed in Ray.

Thanks