[Bio-software] Re: Consed: combine amplicons of same individual

Marian Thieme marian.thieme at lycos.de
Mon Oct 9 03:49:53 EST 2006

Hello Bastien,

as you already supposed correctly I have many different individuals. 
Sorry, I didnt point out, that I would like to align each amplicon 
against a reference sequence. Therefore each amplicon can correctly 
placed in the editor/browser. Furthermore I could imagine, that the 
browser combines fragments implicitly, because it only needs to check 
some pattern in the amplicon's filename (for instance) and put all 
amplicons in the same line, where the pattern occurs. Hence we actualy 
dont need to make a big assembly, or not ? and the main task is to align 
all the sequences to a reference sequence, when aligned correctly, then 
the sequence of each individual should assembled implicitly. Make sense ?
(I also tested staden package a little bit, but I found it difficult to 
incorporate a reference sequence, because you first need to create trace 
files in both directions, but I dont think this makes much sense, 
because I get the reference sequence as fasta file without trace data. 
Unlike staden, consed is able to do that (with crossmatch))

Bastien Chevreux schrieb:
> Marian Thieme wrote:
>> I have a question about the Alignment und Sequence editor Consed,
>> because I want to evaluate and compare some sequence analysis tools to
>> find out which one is best suited for a resequencing project: Is it
>> possible to combine fragments/amplicons so that I get a contiguous
>> sequence. I could imagine, that all fragments of a certain individual
>> are placed in one line, so I can easly browse and edit the sequence for
>> each individual. (Perhaps, overlapping fragments should be merged in
>> some way). (At the moment I havent managed that, so all amplicons are
>> treated seperatly.)
> Hi Marian,
> do you have sequences from one individual or from several? In the later
> case, I am not sure whether there is a package that has exactly what you
> want out of the box. In any way, consed (the editor) alone will probably
> not help you as you would need an assembler (e.g. mira, phrap, cap3, etc.)
> to go along with it.
> Have you looked at the Staden package (http://staden.sourceforge.net/)? It's
> *the* "swiss-army-knife" of assembly tools and is used for very small and
> very large projects (millions of sequences). It has 
> - a nice preprocessing package (pregap)
> - a powerful editor (gap4 for contig editing, joining, splitting, annotation
>   and much more) 
> - and a number of very useful tools to complement certain needs (mutation
>   detection etc.).
> It also has some simple assemblers integrated, external assemblers can be
> plugged into quite easily.
> In your case, I could imagine that letting assemblers run on subsets of your
> sequences (each one containing sequences from exactly one individual)
> combine the results within gap4 might be what you need.
> Regards,
>   Bastien

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