README.txt --> this file

All the genomes were dwnloaded on date 12.10.2018

Zipped files with [GROUPS]_[TYP]_[QUAL]_genomes.[PROGRAM].zip naming scheme are
prebuilt indices of reference genomes downloaded from RefSeq that can be used
for read mapping using a read mapper [PROGRAM].

[GROUPS] is/are one of A, B, F, and G or a combination of these.
  Where:
     A = Archaea
     B = Bacteria
     F = Fungi
     V = Viruses

[TYP] is either SP for one reference per species or ST otherwise.  
[QUAL] is either CMP when only complete genomes (including chromosomes) are considered
       	      or ALL when draft genomes are considered as well.  
For example
    ABVF_SP_CMP_genomes.yara.zip  --> A pre-built yara_mapper index containing
    Archaeal(A), Bacterial(B), Fungial(F) and Viral(V) genomes.
    The index contains 1 genome per species and only complete genomes are considered. 
    

[GROUPS]_[TYP]_[QUAL]_genomes.sldb --> a slimm database containing the mapping
from accession to taxon id and other taxonomic information such as names and
a partial taxonomic tree covering the corresponding databases with a similar name
regardless of the read mapping program.

For example
    ABVF_SP_CMP_genomes.sldb can be used together with sam files produced using indices:
         ABVF_SP_CMP_genomes.yara.zip or ABVF_SP_CMP_genomes.bowtie2.zip

SRR1057982.fastq.gz --> a sample metagenomic read file.