get maq map output - maqview application

[fatseq]

Hi people, I´m new here and currently working on my first sequencing data which is Illumina GA2 data. I used maq for the alignments, but now I don´t know how to get the alignment data into a nicer format than the ".map"-files. Is there any tool someone can recommend, like maqview, to visualize the alignments? and how do I get a readable format? I used the "maq mapview" option but this only displays the results to the screen, how can I put the data into a new file? Should I use the "mapmerge"-command to do this?
I would be happy to get an opinion and/or advice on this...although my problems are probably trivial :-) to you. Many thanks!
fatseq

[jkbonfield]

Li Heng maintains a list of alignment viewers at http://lh3lh3.users.sourceforge.net/NGSalnview.shtml

You may also want to consider changing it from maq to sam/bam format for some tools, depending on precisely what you want to do downstream.

James