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Old 06-03-2009, 06:14 AM   #1
mjleaks
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Default 454 assembly using consed

Has anyone assembled 454 data with consed package version 19? I'm having some issues with reading of the .sff files and wondering if anyone has completed an assembly of 454 read data (not using Roche software produced .ace files). I'm using "add454Reads.perl reference.ace sff.fof reference.fa", where the fof specifies the sff files to assembly, but although the script runs, I get an error "doesn't existile /shared/BNFinal/mapping/consed/sff_dir/FPDLD6P02.sff", and the 454 reads are not brought into the assembly; it basically assembles with only the reference sequence. I also tried specifying just the names of reads that I want to bring in to the assembly; these exist in the sff files in the corresponding sff_dir directory to the edit_dir I am running the assembly from. Someone mentioned needing to update phrap, which I will look into, but any other thoughts on this (I'm sure I'm missing something obvious)?
Thanks,
Liz
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Old 06-03-2009, 11:49 AM   #2
bio-x
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I have successfully assembled 454 data with consed version 19? sff.fof contains the pathway of *.sff file. do you have the permission to access the sff file?
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Old 06-03-2009, 11:56 AM   #3
mjleaks
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Thanks for the response. Could you give an example of the contents of the sff.fof file? I checked permissions, but will check again!
Liz
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Old 06-03-2009, 12:00 PM   #4
bio-x
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the content is :
../sff_dir/FPDLD6P02.sff
sff.fof, add454Reads.perl, reference.ace reference.fa are all in edit_dir.
if your reads are too much, you need use cross_match.manyreads

good luck
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Old 06-03-2009, 12:10 PM   #5
mjleaks
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Well still not sure what I'm doing wrong. The permissions for the files and directories are fine. The sff.fof file itself seems to be fine; the contents are being read. The sff file looks normal (can load it into other apps etc.), and the path is correct..... Thanks!
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Old 06-03-2009, 12:43 PM   #6
bio-x
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add454Reads.perl command is "consed". Have you change consed_linux64bit to consed?

Last edited by bio-x; 06-05-2009 at 05:55 AM.
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Old 08-27-2009, 10:53 PM   #7
ajaybioinfo
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Dear sir!, bio-X

please tell me how to configure the consed 19 for the assembly of 454.sff file , as it was 6 month i am trying to assemble but cannot get the success .

sir please tell the procedure how to configure the phred ,phrap and consed to assemble, .sff files

and the necessary version needed for the assembley of the .sff files..please sir it was great help for me. as my boss is annoyed on me very much

i shall be very thankful to you

waiting for your kind reply please mail me
ajaybioinfo@gmail.com
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Old 08-28-2009, 02:52 AM   #8
sklages
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Quote:
Originally Posted by ajaybioinfo View Post
Dear sir!, bio-X
please tell me how to configure the consed 19 for the assembly of 454.sff file , as it was 6 month i am trying to assemble but cannot get the success .
What have you tried? What problems occured? Have you carefully read the documentation supplied with the package (http://bozeman.mbt.washington.edu/co...EADME.19.0.txt)?

Quote:
sir please tell the procedure how to configure the phred ,phrap and consed to assemble, .sff files
Again, have you read the docs?


Quote:
and the necessary version needed for the assembley of the .sff files..
You should use at least consed v19.xx and cross_match version 1.080806 or higher.

Assembling 454 data with consed usually means "reference guided" assembly, not de-novo. You should keep that in mind.

cheers,
Sven
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