add mm39 genome index?

[microbemarsh]

Hi @bede,

Great work on hostile, its very user friendly and nice for human microbiome research, however my group does some mouse microbiome research and I was wondering if you had thought about adding any other additional indexes to the list. I saw you're looking to do a new release soon and wanted to add my two cents!

Thanks, Austin

[bede]

Hi Austin, Thanks for your message. Are you aware that you can supply custom indexes already? If dehosting long reads you can provide a path to a fasta file instead of an index name. For short reads you'll need to build a bowtie2 index, e.g. bowtie2-build genome.fa index-name which can be referenced in similar fashion (see README for details). Would you specifically like to see a standard (prebuilt) Hostile index for mouse available in object storage? I appreciate that this is more convenient and can consider adding it.

Thanks, Bede

[microbemarsh]

In the case of using a custom index on long reads, is it essentially just finding the alignments with minimap2 and removing those regions from the output fastq? And it might be useful to users later on to have the prebuilt mouse index available but if I'm the first to request it I would say its not too pertinent to add it.