refseq.md

Building a Database from NCBI RefSeq Genomes

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.

Custom RefSeq Database Builds

MetaCache comes with the following helper scripts:

• download-ncbi-genomes downloads NCBI reference genomes
• download-ncbi-taxonomy downloads NCBI taxonomy
• download-ncbi-taxmaps downloads NCBI accession to taxon ID maps (not needed for the latest NCBI RefSeq releases)

Example

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

See also

• Output Formatting
• Building Custom Databases
• Using Partitioned Databases

Command Line Options

• for mode build
• for mode query
• for mode merge