These files are too big to include with BBMap, but are available for download individually at http://portal.nersc.gov/dna/microbial/assembly/bushnell/

BBSketch sketches of Refseq, encoded using k=31,24
refseq_sketch.tar.gz

Common ribosomal kmers from Silva 132.  Primarily for use in metatranscriptome ribosomal filtering with BBDuk.
Created using bbmap/pipelines/makeRiboKmers.sh
riboKmers.fa.gz

Taxonomic tree, updated regularly.
Created using bbmap/pipelines/fetchTaxonomy.sh
tree.taxtree.gz

Masked version of mouse reference, for removing mouse contaminant reads.
mouse_masked.fa.gz

Masked version of cat reference, for removing cat contaminant reads.
cat_masked.fa.gz

Masked version of dog reference, for removing dog contaminant reads.
dog_masked.fa.gz

Masked version of human reference, for removing human contaminant reads.
hg19_masked.fa.gz

Masked version of common bacterial contaminants, for removing bacterial contamination from eukaryotes.
fusedEPmasked2.fa.gz

Masked version of common bacterial contaminants, for removing bacterial contamination from bacteria. (This is the same organisms as above, but more heavily masked for sequence shared with with other non-contaminant bacteria)
fusedERPBBmasked2.fa.gz
