I have a Hi-seq Single end data and want to align it to a viral genome and
have fasta file of viral genome. I have created index files out side Galaxy
(I believe I cannot create index file with in Galaxy). The question which I
have is:

There are various index files (v.fasta.amb; v.fasta.pac; v.fasta.rbwt;
v.fasta.rpac; v.fasta.sa) should I be using all the these files as zip file
for index file or one (which one?).


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