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I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one ncbi_database.zip file which contain 2 folders and 3 files of doc,assembly_report_json file. I read one file named read.md which came after downloading but its not helping. What should be done in this case?

I don't have an issue with using bwa-mem; the problem is with the reference genome from NCBI. I downloaded it from https://ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1 but after that I checked the downloaded file and I got 5 folders into it and I'm confused which one to use. 2 files have .fna extension and the rest are reports that are in the json file format.

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    $\begingroup$ Welcome to the site @moon. My role is to try to get the questions as clear as possible. Firstly it's worth noting bwa-mem2, but you want to try getting bwa mem working first. The read.md will just be the installation instructions. Are you looking for the manual? Is the following helpful, hcc.unl.edu/docs/applications/app_specific/bioinformatics_tools/… and follow the bwa mem instructions. Maybe try it and then post back on specifically what the problem is, e.g. the error message? $\endgroup$
    – M__ ♦
    Commented Aug 2, 2023 at 13:22
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    $\begingroup$ The answer by @atpoint is the best answer to the question as the question is written right now. My advice is to consider accepting this and further questions can then be asked. This Lepidoptera genome assembly and a reference genome is definitely needed. $\endgroup$
    – M__ ♦
    Commented Aug 2, 2023 at 21:48
  • $\begingroup$ Only accept answers if they solve the problem you're having. If the answers don't match your problem, feel free to clarify the question to explain further. $\endgroup$
    – gringer ♦
    Commented Aug 4, 2023 at 0:16

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What you need is the genome sequence in fasta format, typically suffixed .fa, for example from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/

This file needs to be indexed via bwa index.

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I downloaded genome from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/ I got 5 files in it so if you are confused which one to use in that so GCF.fna having genomic data with fna extension is used as an reference genome if you are also new to this things this might be useful.

Thank you

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  • $\begingroup$ Please accept the other answer as well, as it addressed your question and was given before you added your own answer and accepted just the one you added $\endgroup$
    – Ram RS
    Commented Aug 7, 2023 at 14:29

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