Genestrip-DB - a selection of databases for Genestrip

This project contains some configuration files and two scripts in order to generate databases and indexes for metagenomic analysis via Genestrip.

License

Genestrip-DB is free for any kind of use. However, the associated software, Genestrip, has a more restrictive License.

Building and installing

Genestrip-DB requires Maven 2 or 3 and the JRE 11 or higher.

To build the databases and indexes, cd to the installation directory genestrip-db. Given a matching Maven and JDK installation, sh bin/makedbs.sh will generate 9 databases (and indexes) of different sizes. The generation process is resource intensive and may take several days for all databases. Generating the bacterial databases is particularly time consuming.

Your machine should have:

• 1.5 TB of free disk space - mainly for downloading genomes from NCBI,
• at least 8 cores - the more the better (some phases of the database generation keep 32 cores 100% busy),
• 48 GB of main memory,
• a high bandwidth Internet connection.

The databases are based on and compatible with Genestrip v2.2.

The databases

All databases are genomic or based on total RNA.

Name	Category	Description	Database disk size	Sources and references
babesia	protozoa	Babesia species from the RefSeq and Genbank which are potentially pathogenic for humans	N/A	General knowledge
borrelia	bacteria	Borrelia species from the RefSeq and Genbank	N/A	General knowledge
borrelia_plasmid	plasmid	Borrelia species from the RefSeq and Genbank	N/A	General knowledge
tick-borne	bacteria	Tick-borne infections from the RefSeq which are potentially pathogenic for humans	N/A	General knowledge, partially collected from Armin Labs
tick-borne_rna	bacteria	Same as tick-borne but based on total RNA.	N/A
human_virus2	viral	Viruses from the RefSeq and Genbank which are potentially pathogenic for humans	N/A	Extracted from the Viral Zone
parasites	invertebrate	Parasitic invertebrate animals from the RefSeq which are potentially pathogenic for humans	N/A	Collected from the book "Die Parasiten des Menschen" by Heinz Mehlhorn
protozoa	protozoa	Protozoan parasites from the RefSeq which are potentially pathogenic for humans	N/A	Collected from the German book "Die Parasiten des Menschen" by Heinz Mehlhorn
protozoa_rna	protozoa	Same as protozoa but based on total RNA	N/A
vineyard	fungi	Fungal infections of grapevine taken from the RefSeq and Genbank	N/A	Collected from the German book "Rebschutz" by Walter Hildebrand, Dieter Lorenz and Friedrich Louis
plasmopara	plant	Peronosporales as infections of grapevine taken from the RefSeq and Genbank	N/A	Collected from the German book "Rebschutz" by Walter Hildebrand, Dieter Lorenz and Friedrich Louis
fungal_infect	fungi	Fungal infections of humans from the RefSeq and Genbank	N/A	Collected from the German book "Rebschutz" by Walter Hildebrand, Dieter Lorenz and Friedrich Louis

Note that Genestrip's updateddb-phase accounts for unspecific k-mers and largely avoids false positive counts during matches. To further reduce false positives, all databases except for vineyard, chronicb-rna and protozoa-rna are built such that k-mers also occurring in the human genome are pushed to the least common ancestor.

Testing the databases borrelia, borrelia_plasmid and chronicb

The script bin/matchticks.sh runs the Genestrip goal match for 8 fastq files taken from this publication. To do so, the fastq files will be streamed from the corresponding NCBI server. As expected, Genestrip finds DNA from borrelia and other tick-borne infections accordingly.

Downloading the ready-made databases

If you don't want to generate them yourself, the databases and indexes can also be downloaded from genestrip.it.hs-heilbronn.de. The projects folder corresponds to the projects folder's state of this project, after the scripts bin/makedbs.sh and bin/matchticks.sh have run successfully on the RefSeq Release 230.