Can I quickly retrieve a small region from the maq alignment?
Yes, you can. Maqview provides a command-line tool, maqindex, to do this. • Are there similar alignment softwares that specifically designed for short reads? Eland, the Solexa read alignment program, can do this. It is faster than Maq actually. Maq deliberately trades the speed for several things that are not implemented in Eland. I know people also use SSAHA2, GMAP, Mosaik and SXOligoSearch to align reads. A friend of mine, Ruiqiang Li, wrote a software, SOAP, which is capable of finding short indels. On smaller data set, cross_match may also be a worthy candidate. You can use cross_match to map unmapped reads to find indels.
