Use the metacache-build-refseq script to build a MetaCache database based on complete bacterial, viral and archaea genomes from the latest NCBI RefSeq release:
git clone https://github.com/muellan/metacache.git
cd metacache
make
./metacache-build-refseq
Note that the genomes will be downloaded first, which can take some time.
Once the default database refseq is built you can classify reads:
./metacache query refseq myReads.fa -out results.txt
./metacache query refseq anyFolderWithFastaOrFastqFiles -out results.txt
./metacache query refseq myReads1.fa myReads2.fa -pairfiles -out results.txt
./metacache query refseq myPairedReads.fa -pairseq -out results.txt
Option -pairfiles means that paired-end mates are stored in two different files so that read number 20 from file 1 is the mate of read number 20 from file 2.
Option pairseq means that paired-end mates are stored in the same file so that reads 1 and 2 are mates, reads 3 and 4 are mates and so on.
MetaCache comes with the following helper scripts:
download-ncbi-genomes downloads NCBI reference genomesdownload-ncbi-taxonomy downloads NCBI taxonomydownload-ncbi-taxmaps downloads NCBI accession to taxon ID maps (not needed for the latest NCBI RefSeq releases)Build a database with bacteria, viruses, plant and fungal genomes from RefSeq:
./download-ncbi-taxonomy tax_folder
./download-ncbi-genomes refseq/bacteria genomes_folder
./download-ncbi-genomes refseq/viral genomes_folder
./download-ncbi-genomes refseq/plant genomes_folder
./download-ncbi-genomes refseq/fungi genomes_folder
./metacache build myrefseq genomes_folder