I have an ace file generated by amos2ace, but it can not be opened by consed. what i want is a phd file coming from the ace file. So can any tools convert the ace file to phd file?
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RE: how convert ace to phd without consed?
Consed comes with several utility programs:
ace2Fasta.perl generates a fasta file (actually I think it is fastq)
then
fasta2Phd.perl would give you the phd file you want.
You need to get these from the good people at U. Washington though.
Tom K
OHSU -
I got consed v19, and mapped the Solexa reads to my reference sequence. It work well. But I had more two hundred contigs and how can i convert the ace file to phd files seperately by consed/phrap at one time? I saw that every contig could consert to phd file by file->export consesus sequence with options.Comment
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Viewing Ace Files
There are several open source software to view the alignments in the assembled contigs: Eagleview (Marth Lab, Boston College). More are listed in other posts. If you want to edit and manipulate the contigs try the commercial software Lasergene SeqMan from DNAStar. Both programs have trouble with large numbers of reads. I don't know how Consed works with 5 Mio reads (or more) aligned to a reference sequence.Comment
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I want to convert ace file which contains thousands contigs to phd file at one time by consed, is there any good way?Comment
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I've no idea about consed... but we can use BioPerl for this...
see this link for more on this... http://www.bioperl.org/wiki/Module:Bio::SeqIOComment
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@anyone1985,
ace format is an alignment format, phd isn't. What do you want to achieve?
You have mapped your solexa reads against a reference sequence and get a few thousand contigs? Optimise your reference
If you just want to reassemble your contigs, convert ace to fasta and use phrap and/or cap3 directly?
SvenComment
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I just assemble my solexa data with velvet, and get about 240 contigs larger than 500. Then, I map the solexa data to the contigs using the consed/addSolexaReads.perl to get a contigs with quality. Now, I want to convert the ace file to phd file individually. The consed can export the phd file only one at a time, I just want to know how to convert it all at a time.Comment
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Well, I think you need to write a script on your own, which parses the ACE files and dumps PHD. That's probably the fastest way. No other idea, sorry.
SvenComment
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thanks^^^^^^^^^^^^^^Comment
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What's Consed's memory usage when open ACE file contains 10 million solexa reads ?
Who knowns the memory usage about Consed?Comment
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To be honest, I maped my reference sequence with about 7 million reads, which is about half of my data. I divided the reference into six files, and the server that i use worked well. If i put them together, the program would be killed. My server is inspur with 8 G menory, about 4 G swap.Comment
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v19.00, 32b PE, 6min to open, didn't check cpu timeOriginally posted by baohua100 View PostComment
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