Originally posted by sklages
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Originally posted by sklages View PostCelera Assembler has been optimised for at least 454FLX length reads; I have used it for shorter GS20 as well, but it may fail. All these assemblies were hybrid assemblies, not 454-only ones.
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@Dan,
my suggestion was to either use the bambus mate pair output or a TraceArchive formatted XML file for use with "toAmos", like
$ toAmos -s x.fasta -q x.qual -m test.mates -o test.a.afg
or
$ toAmos -s x.fasta -q x.qual -x test.xml -o test.a.afg
but, of course, you have to create these files before.
It is probably the easiest way to write your own "your_data2TraceArchive.pl" and then convert it to whatever you want, e.g. CA format using "tracedb-to-frg.pl".
@new300,
Celera Assembler has been optimised for at least 454FLX length reads; I have used it for shorter GS20 as well, but it may fail. All these assemblies were hybrid assemblies, not 454-only ones.
hth,
Sven
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Are you planning to use the Celera assembler with short reads? Because I don't think it would work very well.
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Input files for the Celera Assembler?
Hi,
I have sequence reads as a fasta file with a fasta quality file. I am converting these into .frg input for the Celera Assembler (CA) using AMOS,
Code:toAmos -s test.fasta -q test.qual -o test.afg
Code:amos2frg -i test.afg
However, the above strategy does not recognize the 'mate pairs' in my data (paired end reads) that are 'linked' using the St Louis naming convention (basically read0012.b is pared with read0012.g, the .b and the .g denoting the forward and the backward read, respectively).
On the AMOS mailing list I got a reply to a similar question from Sven Klages, which told me that CA is usually passed a separate "linkage information" file in addition to the .frg input created above. His suggestion was to create linkage data in 'Trace Archive' format*, and then convert that to input for CA using AMOS again.
Has anyone tackled this problem before? Is there any code 'off the shelf' to create the mate pair data?
* http://www.ncbi.nlm.nih.gov/Traces/t...#header-global
Cheers,
Dan.
P.S. Any other good mailing lists for sequence assembly?
If you know any, I'll add them here:
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