I have not maintained maq for quite some time. Most of my time on sequencing related tools goes to samtools and bwa. I usually recommend people to use these tools (and other better tools) rather than maq. This does not mean maq is not accurate any more. On the contrary, several independent evaluations show that maq's alignment and SNP calling accuracy is still among the top few. What maq is missing is the speed of more recent aligners and the native SAM output.
That is saying: if you are happy with maq, you may continue to use it and do not worry maq is something substandard; if you need shining new features absent from maq or feel maq is too slow or maq2sam+fixmate is clumsy, try bwa/novoalign+samtools/picard/gatk/....
That is saying: if you are happy with maq, you may continue to use it and do not worry maq is something substandard; if you need shining new features absent from maq or feel maq is too slow or maq2sam+fixmate is clumsy, try bwa/novoalign+samtools/picard/gatk/....
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