bowtie2

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Link to download FASTA files matching the GRCh38 bowtie2 indexes, currently returns an error: ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj.fa.gz

In fact, the whole FTP server seems out of commission at the moment.

Is this a known problem that will hopefully get fixed eventually? In the meantime, is there any other way to get ahold of this FASTA file?

Thanks in advance!

Some of the links in the sidebar need to be updated; I will be doing so tomorrow. In the meantime the index in question can be found at this link: https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj.zip .

Disregard my previous comment as the file in question has not been moved to AWS just yet. We are looking into the FTP server issue. During this downtime grch38_1kgmaj.fa can also be generated by running the bowtie2-inspect on the index files obtained from the link previously posted.

@ch4rr0 Thanks for looking into this: the problem seems to have been resolved and I was able to download the fasta file (I had a brief look through the scripts, but couldn't quite figure out what input/script combination would produce the right fasta file).

On a somewhat tangentially-related topic: is there a log somewhere of the changes that were made to the nomenclature used? Comparing with files that were aligned about 1y ago, I've noticed that chromosome names have seemingly been changed again at some point…?

@zedrdave, you can check out this README for more information on the naming convention and changes made. I hope this helps.