Downloads NCBI genomes for Mash and puts taxonomic information into the references comments. Very barebones and slow at the moment, adjust to your own needs. Download sequentially genomes from all RefSeq domains. Meant to be used with mash taxscreen (fbreitwieser/Mash).
# download all Refseq genomes, build min-hashes (takes days)
$ perl dl-genomes.pl run
# Combine all archaeal sketches into one pooled sketch
$ mash paste archaea -l <( find sketches-k21s1000/archaea/ -name '*.msh')
# ID field of the sketch contains assembly info, comment contains taxonomy ID
$ mash info archaea.msh
#Header:
# Hash function (seed): MurmurHash3_x64_128 (42)
# K-mer size: 21 (64-bit hashes)
# Alphabet: ACGT (canonical)
# Target min-hashes per sketch: 1000
# Sketches: 873
#
#Sketches:
# [Hashes] [Length] [ID] [Comment]
# 1000 2947156 GCF_003201835.1 Acidianus brierleyi, CompleteGenome assembly [2.95 Mbp, 1 seqs] taxid 41673
# 1000 2137654 GCF_000213215.1 Acidianus hospitalis W1, CompleteGenome assembly [2.14 Mbp, 1 seqs] taxid 933801
# 1000 2287077 GCF_003201765.1 Acidianus sulfidivorans JP7, CompleteGenome assembly [2.29 Mbp, 1 seqs] taxid 619593
# Make a test file
$ zgrep -h -A1 '^>' genomes/archaea/*/*.gz | grep -v '^--' > archaea-test.fa
# Download NCBI taxonomy
$ wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
$ tar xvvf taxdump.tar.gz
# Create Kraken-style taxonomic report with fbreitwieser/Mash
$ mash taxscreen archaea.msh archaea-test.msh
% hashes taxHashes hashesDB taxHashesDB taxID rank name
100.0000 557 0 448901 0 no rank 1 root
100.0000 557 0 448901 0 no rank 131567 cellular organisms
100.0000 557 3 448901 300 superkingdom 2157 Archaea
84.5601 471 1 372025 228 phylum 28890 Euryarchaeota
56.7325 316 0 253546 140 no rank 2290931 Stenosarchaea group
48.1149 268 38 186986 6523 class 183963 Halobacteria
24.7756 138 14 71202 1074 order 1644055 Haloferacales
11.6697 65 9 31337 454 family 1644056 Haloferacaceae
6.6427 37 18 10148 3304 genus 2251 Haloferax
1.2567 7 7 799 799 species 1544718 Haloferax sp. SB29
0.5386 3 3 55 55 species 2077201 Haloferax sp. Atlit-19N
0.3591 2 2 260 260 species 2077203 Haloferax sp. Atlit-12N
0.1795 1 0 147 0 species 2246 Haloferax volcanii
0.1795 1 1 147 147 no rank 309800 Haloferax volcanii DS2