I am working with gap4 in Berlin, Germany, and am looking for an
algorithm and/or script. It should deal with the following:
How are two contigs brought into order? I mean, if there is no
connection between them. How do you know that two reads (of two
different contigs) match, how do you exclude wrong results? The idea
seems to be clear, but I wonder if any realization already exists.
Thanks in advance, moritz