kraken-trawl: A tool to help you build custom kraken databases

Use case

kraken is a tool for rapid identification of species from short read data (Wood and Salzberg 2014). It uses a kmer database, with kmers identified by their NCBI Taxon ID. It comes with a few databases preconfigured, but sometimes they are not enough, and they are also significantly out of date.

While kraken provides for a limited API to build your own, custom, database, it leaves it up to the user to find the sequences of interest, and rename them in an appropriate way so that the kraken-build tool can interpret the sequences correctly.

What kraken-trawl aims to do is to automate as much as possible the creation of custom kraken databases. The user only needs a list of species names of interest. kraken-trawl will then download the genomes, if available, transform them to the appropriate name, and place them in a folder structure appropriate for kraken-build. The user can create a new DB from scratch, or add to an existing DB.

Dependencies

Kraken

kraken-trawl depends on kraken. Download and installation instructions can be found here.

Aspera

The current version assumes you have aspera ascp installed and in the path. It also assumes that you have an environmental variable called ASPERA_KEY that points to the aspera key for downloading from NCBI. For a guide on obtaining ascp and a key from NCBI go here.

Python

kraken-trawl also depends has the following python dependencies:

• python 2.7
• BioPython
• pandas >=0.19
• click >=5

Installation

The easiest way of installing kraken-trawl is using pip:

pip install git+https://github.com/andersgs/kraken-trawl.git

Use the --user option to install locally (by default in $HOME/.local/bin):

pip install --user git+https://github.com/andersgs/kraken-trawl.git

Use the --install-option to install the script in a particular location (say you have some other folder on your PATH where you store scripts):

pip install --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/andersgs/kraken-trawl.git

Once installed type the following:

kraken-trawl --help

Configuration

The current version relies on an environmental variable to work properly:

• ASPERA_KEY

Either type the following before using kraken-trawl, or paste this line in to your bash_profile:

export ASPERA_KEY=/path/to/asperakey/aspera_key.openssh

You may ask, why am I using environment variables for configuration? The reason is that this is currently considered best practice in tool development. More here: 12factor app.

Options

Usage: kraken-trawl [OPTIONS]

Options:
  --assemb_file TEXT        assembly_summary file
  --kraken_db TEXT          name of kraken db                                                                                                         -c, --create TEXT         create a new database at path <give path>
  --kraken_db_path TEXT     path to kraken db                                                                                                         --taxon_list TEXT         give it a taxon list to filter the
                            assembly_summary.                                                                                                         --include_human           include the human reference genome
  --filter_opt TEXT         Can be all, strict, moderate, or liberal.                                                                                 --outdir TEXT             Where to place downloaded genomes.
  --no_log                  Do NOT output a tab-delimited list of genomes                                                                                                       added
  --do_not_inject_adapters  Do **not** add Illumina adapter and primer
                            sequences to DB
  --threads INTEGER         How many threads to use when building the database
  --kmer_len INTEGER        kmer length to use when building database
  --minz_len INTEGER        minimizer length to use when building database
  --clean                   clean db of unnecessary files after making the DB
  --help                    Show this message and exit.

Output

1. A series of folders each containing a *.genomic.gbff.gz file. Because we are using aspera if the folder structure is maintained, only novel genomes will be downloaded subsequently.
2. an aspera_src_dest.txt file containing the SRC and DEST for each genome. This file is used to for the aspera download .
3. individual genome *.fna files in the <kraken_db>/libraries/added folder.
4. a log file, with a tab-delimited information on each downloaded file:
   • Organism --- the organism name, including any strain names
   • Accession --- the accession id
   • RefSeq --- the RefSeq category, if any
   • Assembly Level --- the assembly level (i.e., Complete Genome, Chromosome, Scaffold , or Contig)
   • Source --- the location of the genbank file on the NCBI servers
   • Destination --- the local folder with the genbank file
5. a missing_taxon.txt --- a list of taxons for which no genomes were found

Examples

History

Missing Features

References

Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46 URL