I have Illumina reads of a bacterial genome and was able to assemble many parts of it. Now I also found Sanger and 454 data for the same strain. Is there a pipeline, that can handle all these data including trimming and error correction?
MIRA probably can handle every type of data and do everything for you. There are just two problems:
1) taming MIRA: it has lots of options getting the best setting can be daunting - read its wiki and user guide carefully.
2) the latest release (something like 4.9.6beta, but was really stable) seems to have disappeared, and you will have to use MIRA 4.0.2.