assembly archive (gap2ace, gap2xml)

mbs_
2006-03-24
2013-04-18
  • mbs_
    mbs_
    2006-03-24

    Dear all,

    we plan to submit our gap4 projects at the assembly archive @ncbi and are looking for tools that can handle this.
    The NCBI people have a support for ace files (ace2xml), like they seem to come out of consed.
    Has anyone a procedure or programs that are able to either
    1. generate an XML file ready for the submission out of a gap4 project (haha, only joking!), or
    2. convert the gap assembly to ace by some way?

    We tried gap2caf and got the project.caf file but when calling
    caf2ace < project.caf > project.ace
    the program crashes either right away (Segmentation fault) with an empty output or after a few lines with the same error.

    We tried LINUX and Solaris, different compilers, unfortunately all with the same frustrating result.

    Any idea? Please!

    Markus