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?