Databases

Markers

Autometa comes packaged with the necessary markers files. Links to these markers files and their associated cutoff values are below:

• bacteria single-copy-markers - link

• bacteria single-copy-markers cutoffs - link

• archaea single-copy-markers - link

• archaea single-copy-markers cutoffs - link

NCBI

If you are running Autometa for the first time you will need to download the NCBI databases. You may do this manually or using a few Autometa helper scripts. If you would like to use Autometa’s scripts for this, you will first need to download Autometa (See Installation).

# First configure where you want to download the NCBI databases
autometa-config \\
    --section databases --option ncbi \\
    --value <path/to/your/ncbi/database/directory>

# Now download and format the NCBI databases
autometa-update-databases --update-ncbi

Note

You can check the default config paths using autometa-config --print.

See autometa-update-databases -h and autometa-config -h for full list of options.

The previous command will download the following NCBI databases:

• Non-redundant nr database

  • ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz

• prot.accession2taxid.gz

  • ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz

• nodes.dmp, names.dmp and merged.dmp - Found within

  • ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

After these files are downloaded, the taxdump.tar.gz tarball’s files are extracted and the non-redundant protein database (nr.gz) is formatted as a diamond database (i.e. nr.dmnd). This will significantly speed-up the diamond blastp searches.