I need to compare multiple sequences in fq format to multiple library sequences. The range of sizes will be between 10Kbp and 100Kbp which should I use? Bowtie, Bowtie2, Mauve, MUMmer, Mugsy?

I am having trouble finding HOWTOs on some of these.

If I use Mauve, how do I convert .fq to .gbk?

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