FastQ aligner

[emlas]

I have to pipe the Illumina MiSeq FastQ files through an aligner to get the BAM files. Could you please advice which program to use.

[GenoMax]

You could basically use any NGS aligner. bwa, BBMap, bowie2 etc. You will need to use "samtools" to convert the resulting SAM alignment files into BAM (binary) format. You would want to do some basic QC using FastQC before you start doing the alignments though that is strictly not necessary.