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Old 02-10-2009, 04:31 PM   #1
phageman
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Location: Australia

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Default Viewing paired-end inconsistencies in 454 scaffolds

Greetings
We are attempting to sequence microbial genomes with paired-end 454 data supplemented with Illumina/Solexa GAII data to resolve homopolymers etc. Newbler assembly of the 454 data has generated some very nice scaffolds but I have detected at least one inverted contig. I was wondering if anybody knows a means of viewing the Newbler output that will show the paired end relationships as a means of detecting those that are inconsistent. It seems to me that the ACE file does not include scaffold information and Newbler generated scaffolds are simple multifasta files. Any assistance would be most appreciated.

Cheers and thanks
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Old 02-11-2009, 12:52 AM   #2
andpet
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Default Viewing paired-end inconsistencies in 454 scaffolds

Hi,

have a look at the AMOS assembly package (http://amos.sourceforge.net/). It contains a script called amosvalidate that checks for such inconsistencies in assemblies
(also described in this paper http://www.ncbi.nlm.nih.gov/sites/en...earch=18341692).

The package also contains Hawkeye, a nice assembly viewer, that can visualize these inconsistencies and that is fast enough for displaying next generation sequencing data (at least for small assemblies).

However installation of the amos package is a little bit tricky ...

Greets,

Andreas
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Old 02-17-2009, 12:31 PM   #3
hlu
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Default

Quote:
Originally Posted by phageman View Post
Greetings
We are attempting to sequence microbial genomes with paired-end 454 data supplemented with Illumina/Solexa GAII data to resolve homopolymers etc. Newbler assembly of the 454 data has generated some very nice scaffolds but I have detected at least one inverted contig. I was wondering if anybody knows a means of viewing the Newbler output that will show the paired end relationships as a means of detecting those that are inconsistent. It seems to me that the ACE file does not include scaffold information and Newbler generated scaffolds are simple multifasta files. Any assistance would be most appreciated.

Cheers and thanks

Have you looked at the newbler outout file "454PairStatus.txt"?
This file prints all the pair reads status and coordinates for the assembly. It does not have all the nice pair info on ace file, but at lease it gives pair information there.
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