<p>Hello,</p>

<p>I&#39;m wondering whether there is a program that could calculate chromosome sizes from any fasta file? The idea is to generate a tab file like the one expected in bedtools genomecov for example.</p>

<p>I know there&#39;s the fetchChromSize program from UCSC, but not all genomes are available over there (I need TAIR10 for instance). I&#39;ve read <a href="https://www.biostars.org/p/16396/">this topic</a> already.</p>

<p>I would like a tool that can deal with any genome regardless of the database. If it doesn&#39;t exist I guess it&#39;s possible to just parse fasta files, but I&#39;d be surprised if no one else had done it before!</p>

<p>Cheers</p>

    pip install pyfaidx
    faidx input.fasta -i chromsizes > sizes.genome

That's what you're looking for if you want to use `bedtools genomecov`, but you can transform to a BED file as well using `-i bed`.