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It helps to set up environmental variables to avoid having to type long paths. Here a set of short reads ( myreads.fq) are mapped to the mouse genome (mm10) with a SAM formatted file as output. Note that bwa uses genome.fa as a reference index name and the bwa mem analysis is used. See the BWA documentation for other ways to invoke bwa.
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Similarly, environmental variables can be set up, and in the case of bowtie2 a BOWTIE2_INDEXES variable must be set also. Here we have an example of a paired end analysis, with minimal options. See the bowtie2 documentation for a complete set of command options. Note Bowtie2 uses genome as reference index name (-x genome ).
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