Where I can download index files for Rousettus aegyptiacus?

Question

[mathavanbioinfo]

Hell friends, I need index files of Rousettus aegyptiacus for HISAT2 assembly, Please share any link are avilable

[ATpoint]

What makes you think that such an index exists if not to be found by a google search? Typically prebuilt indices exist for model organisms, which this bat definitely is not. I suggest you download the reference genome and annotation from NCBI and build the index yourself. The hisat2 manual covers how to do that.

Answer 1

[Matteo Schiavinato]

Index files can be easily generated using hisat2-build <your_reference_file> <basename>. The program comes together withhisat2 and you surely have it installed. It is not recommended to use someone else's indexes unless you know exactly how they were generated, because in hisat2 you can also include other information (such as splicing sites) which might be based on an annotation different than yours.

TLDR; if you have a FASTA reference just pass it to hisat2-build to make your indexes.