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02-25-2009, 09:24 PM
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#1 |
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Junior Member
Location: China Join Date: Feb 2009
Posts: 8
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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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02-25-2009, 10:31 PM
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#2 |
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Member
Location: Seattle, WA Join Date: Apr 2008
Posts: 72
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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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03-01-2009, 07:38 AM
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#3 |
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Member
Location: Germany Join Date: Jul 2008
Posts: 26
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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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03-09-2009, 10:04 AM
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#4 |
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Shaun Jackman
Location: Vancouver, Canada Join Date: Mar 2009
Posts: 15
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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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03-09-2009, 10:06 AM
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#5 |
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Shaun Jackman
Location: Vancouver, Canada Join Date: Mar 2009
Posts: 15
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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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03-10-2009, 02:31 AM
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#6 |
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Junior Member
Location: China Join Date: Feb 2009
Posts: 8
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Great! THX a lot, everybody. I'll try as ur advice and feed back the result.
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03-10-2009, 05:49 AM
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#7 |
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Senior Member
Location: Berlin, DE Join Date: May 2008
Posts: 422
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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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