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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!