Pre-built databases
======

Pre-compiled databases that are ready to be used by individual bioinformatics
programs to accomplish microbial community structural and functional analyses.

Genome sequence databases:

 * Built from concatenated genome sequences (../genomes/all.fna).

 - blastn/: BLAST nucleotide database (format version 5).
   * https://blast.ncbi.nlm.nih.gov/Blast.cgi

 - bowtie2/: Bowtie2 index.
   * http://bowtie-bio.sourceforge.net/bowtie2/

 - minimap2/: Minimap2 indices for long and short reads.
   * https://github.com/lh3/minimap2

 - kraken2/: Kraken2 database (with taxonomy).
   * https://ccb.jhu.edu/software/kraken2/

 - bracken/: Bracken k-mer distribution files for typical short read lengths.
   Should be used with the corresponding Kraken2 database (see above).
   * https://ccb.jhu.edu/software/bracken/

 - centrifuge/: Centrifuge database (with taxonomy).
   * https://ccb.jhu.edu/software/centrifuge/

Protein sequence databases:

 * Built from ORF-translated protein sequences (../proteins/all.faa).

 - blastp/: BLAST protein database (format version 5).
   * https://blast.ncbi.nlm.nih.gov/Blast.cgi

 - diamond/: DIAMOND database (format version 3).
   * https://github.com/bbuchfink/diamond

 - mmseqs2/: MMseqs2 sequence database and precomputed index.
   * https://github.com/soedinglab/MMseqs2

Reference files:

 - qiime2/: Reference files (phylogeny and taxonomy) for QIIME 2.