human_genome_database needs to be updated

[Drishti Kaul]

Hi KneadData users!

I have some skin microbiome data and as a first step, ran KneadData in order to filter out the human host contaminant reads. I looked into the *kneaddata_paired_*.fastq files, and after some downstream species profiling, it seems like even after the host decontamination, there were still a few reads that were human. These were probably chromosomes, mitochondrial genome, etc that aren't present in the scaffolded reference per say.

I ran the same analysis with the most recent human genome ref (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna and built the db using bowtie2-build), and it seems like KneadData had filtered out more contaminant reads, and was completely devoid of the host.

It'd be great if the human_genome reference file could be updated to the most recent version for complete host removal.

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GRCh38_major_release_seqs_for_alignment_pipelines

Thanks,
Drishti

[Josh L. Espinoza]

I agree, I've been using this one for that same reason.  In particular, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.tar.gz