Hi I have a set of reads mapped to a reference sequence, what I what to do is to take the reads that map to one sequence and assemble them in a comtig as best as possible. Then I want to repeat this for thousands of sequence-read sets. I do not want to put this in a regular assember like mira, abyss, etc. because it is an overkill for what I want to do. I also do not want any software messing with my assignment and going its own way. Is there such a command line tool?

Thanks
TASR and SSAKE are traditional bets for this sort of thing, as well as PRICE. Haven't tried Tadpole, as genomax2 suggests, but I'm sure that's worth a look as well - especially as ones I've mentioned aren't going to break any speed records!