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Old 02-25-2009, 09:24 PM   #1
fusu
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Default Any de novo assembly software can produce ace file?

I was used to edit the sequence in consed, so is there any software producing ace file for solexa data?
I've tried Edena, it seems to obtain good assembly result, but having no ace files.

thx.
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Old 02-25-2009, 10:31 PM   #2
mchaisso
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Not that I know of. Now that I'm done fixing bugs (for the near future), I'll try and add this to euler-sr.
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Old 03-01-2009, 07:38 AM   #3
andpet
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I think abyss can produce ace files.

At least the current version contains a perl script "abyss2ace" but I never tested it because it is not very well documented.

Andreas
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Old 03-09-2009, 10:04 AM   #4
sjackman
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Default abyss2ace

abyss2ace isn't very well documented at the moment. I've add some Perl POD --help and --man options for the next release. The brief synopsis follows. To load the resulting ACE file in Consed, use

consed -nophd -ace out.ace

Cheers,
Shaun

SYNOPSIS
KAligner -k K reads.fa contigs.fa >alignments.kalign
abyss2ace reads.fa contigs.fa alignments.kalign >out.ace

DESCRIPTION
Create a Consed ACE assembly from an ABySS assembly. The reads are
first aligned against the contigs using KAligner. These alignments are
then converted to an ACE assembly.
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Old 03-09-2009, 10:06 AM   #5
sjackman
Shaun Jackman
 
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Default ABySS mailing list

On the ABySS web page
http://www.bcgsc.ca/platform/bioinfo/software/abyss

there's a link (albeit not very conspicuous) to the mailing list:
http://www.bcgsc.ca/mailman/listinfo/abyss-users

Cheers,
Shaun
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Old 03-10-2009, 02:31 AM   #6
fusu
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Great! THX a lot, everybody. I'll try as ur advice and feed back the result.
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Old 03-10-2009, 05:49 AM   #7
sklages
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Consed itself writes ACE files ..:

addSolexaReads.perl will use cross_match to align reads against a given reference.
Well, if you'd like to assemble denovo this does not work.

Velvet does write AMOS afg files which can be converted into ACE ..

cheers,
Sven
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