Question: Alignment to ref genome
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You just need to specify the basename (part of the filename common to all of your index files) of index files. For example using genome.fa file as input in hisat2-buil we get these files as output(genome.1.ht2 genome.2.ht2 genome.3.ht2 genome.4.ht2 genome.5.ht2 genome.6.ht2 genome.7.ht2 genome.8.ht2). You just need to specify path to the index directory and basename(genome).
What does the option wrapper means in hisat2?