Hi. We have been using AMOS for the past 2 years, trying to template
454 reads for a new Salmonella strain onto the genome of a related
strain. At first we used AMOScmp and make-consensus. They worked
pretty well, but not as well as we had hoped, which led us to write our
own code, optimized for short 454 reads. The new program is basically a
combination of AMOScmp and make-consensus, but optimized for short 454
reads and their unique error properties (monomer repeats). The program
is finished now, and we'd like to make it available as part of AMOS, if
possible. The main program is written in Java, and there are some
helpful supporting programs written in Perl.
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