GetOrganelle Database

All versions of default databases of GetOrganelle

Default directory

By default, the initialized database will be located at ~/.GetOrganelle. It can be changed, by using the command line parameter --config-dir for a single run, or by using the shell environment variable GETORG_PATH for the entire running environment.

For example, one may change the default database directory into /home/shared/.GetOrganelle by adding

GETORG_PATH=/home/shared/.GetOrganelle
export GETORG_PATH

to /etc/profile for system-wide usage, or to ~/.bashrc for user-wide usage in Ubuntu Desktop, or to ~/.bash_profile for user-wide usage in bash, or to ~/.zshrc for user-wide usage in Zsh

and restarting the shell before initialization.

Option 1 Initialization from Github

By default, get_organelle_config.py will automatically access this repository to download and build the SeedDatabase and LabelDatabase of the latest version. e.g.

get_organelle_config.py -a fungus_mt

Due to the unstable accessibility to Github in some regions, the get_organelle_config.py sometimes fails with connection error (e.g., timeout, sha256_unmatch). However, trying the above command more times will simply work in most cases.

Option 2 Initialization from local files

If Initialization from Github still fails after many trials, download this repository and run get_organelle_config.py with the flag --use-local. Making your own database is feasible if you use the same directory structure but not recommended.

Supposing you want to install version 0.0.1 of embplant_pt and embplant_mt, you can choose any one of the following code blocks to install:

1. Use curl to download the released compressed file (ca. 20 MB -> 80 MB):

curl -L https://github.com/Kinggerm/GetOrganelleDB/releases/download/0.0.1/v0.0.1.tar.gz | tar zx
get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./0.0.1

2. Use svn to download part of the repository (ca. 80 MB):

svn co https://github.com/Kinggerm/GetOrganelleDB/trunk/0.0.1
get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./0.0.1

3. Use git clone to clone the entire repository (ca. 200 MB):

git clone https://github.com/Kinggerm/GetOrganelleDB
get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./GetOrganelleDB/0.0.1

Updates

• 0.0.1.minima A minimal subset of 0.0.1 for test only (GetOrganelle 1.7.6+ required).

• 0.0.1 fungus_nr added

• 0.0.0 Initial version

How to contribute

Welcome to the community!

For generating previous databases, I downloaded all available complete plastomes/mitogenomes or complete nr region from the Genbank, semi-manually cleaned them, masked the simple repeats. However, using all sequences as the default database takes too much space for most users. So I made a customized script, scripts/generate_bowtie2_seed.py, to balance the taxa coverage and the size. The basic idea is randomly picking a set of sequences that can represent/recruit all the candidate sequences given a certain gapping threshold (default: 2000 bp). Then I used the sequence as the seed database and extracted the non-tRNA genes as the label database. Of course, each step should be accompanied by error-proof checking.

Guidelines

1. The sequence header of the seed database should include the Genbank accession numbers.
2. The sequence header of the label database should be in the form of >name type - sequence_info_without_space, e.g. >rbcL gene - Amborella_AJ506156_2. The sequence info should at least include the Genbank accession number.
3. For the seed database, single- and oligo-nucleotide repeats should be masked using Ns to alleviate the computational burden from calling irrelevant reads.
4. After using scripts/generate_bowtie2_seed.py, manually check and replace the representative sequences.
5. For the label database, remember to unify the gene names (e.g., upper/lower cases, abbreviations) and exclude the short genes such as tRNAs.
6. Test the database with a range of WGS from different taxa.

Uploading

Follow the following steps to add the compiled database to the community:

1. fork the GetOrganelleDB repo.
2. duplicate the subdirectory of the latest version and rename it to a newer one.

   e.g. if the latest is 0.0.1, rename the duplicate as 0.0.2

3. add the compiled seed/label databased inside the new subdirectory.
4. send a pull request.