CRISPR-DAV: How to make a reference genome file

Question

[Sowmya]

Hello! I am trying to ascertain the percentage of indels introduced into the target DNA sites of my knockout cell line after I generated it using CRISPR mediated knockout. I amplified this area of DNA using PCR and sent the amplicons for NGS sequencing. Now that I have these sequences, I am trying to detect the indels in the position specified by my guide RNA.

To do this, I am using the following pipeline: CRISPR-DAV (https://pubmed.ncbi.nlm.nih.gov/28961906/ , https://github.com/pinetree1/crispr-dav).

I am running the pipeline using a Dockr container.

In the description of the files required to run the pipeline using my own samples, I see that I am required to make a reference genome file and in my visual studio code environment, I see that there is a directory named Genomes and it has a number of files that I have absolutely no idea of how to create. Posting a screenshot below:

Can someone help me out here? How to create these files? Or were these files generated after the pipeline was run on some example sequences that were provided by the publishers?

Thanks in advance!

[GenoMax]

Looks like this is a standard bwa index. See: https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/21534-explanation-of-bwa-index-files#post201375

You can create the index from your genome file using bwa index.