AlethieG

Adaption of MetaG. Used for implementatin in Wochenende.

False-positive results occur in digital metagenomic sequencing of bacteria. Alethie significantly reduces these and optionally outputs analysis charts as Scalable Vector Graphics.

Get the app

Prebuilt archives with GUI (graphical user interface) are available:

Windows

• With Java (recommended): MetaG-2022.1.0-win.zip
• Without Java: MetaG-2022.1.0-nojava-win.zip

Linux

• With Java (recommended): MetaG-2022.1.0-linux.zip
• Without Java: MetaG-2022.1.0-nojava-linux.zip

Alternatives

Alternatively you can build the app with the source code.

• Release: MetaG-2022.1.0.zip
• Current: MetaG-main.zip

Run the app

For the version without java make sure your JAVA_HOME variable is set to jdk 17+

For self-built version see BUILD.md

Windows

1. Unzip into a folder of your choice
2. Run bin/MetaG.bat

Linux

1. Unzip into a folder of your choice
2. Run bin/MetaG

Settings

In order to achieve the best possible results, you can change settings for how MetaG functions. In the regular version with GUI, the layout elements can be used for this. MetaG.properties is a file, intended to make the same changes. Available in both versions, with or without GUI.

Setting	Specification	Value
DIRECTORY	Path for databases	use \\ or / for folders
BROWSE_SUBFOLDERS	Whether or not subfolders should be searched for files	true or false
BAR_COUNT	Quantity of columns in the diagram	50
MAX_POSITIONS	Upper limit of reads to process	at least 1000, recommended 10000
GRAPH_SCALE	Scale of the diagram	1,2,5,10,20 other scaling is experimental
SVG_OUTPUT	Whether or not to create .svg output files	true or false

Note: MetaG.properties is created automatically on first run.

MetaG.properties could look like the following

#MetaG.properties
#Sat Jan 29 13:26:17 CET 2022
BAR_COUNT=50
DIRECTORY=D\:\\MetaG\\Data\\
MAX_POSITIONS=10000
BROWSE_SUBFOLDERS=true
SVG_OUTPUT=false
GRAPH_SCALE=1

Input

Read data sets from .csv files with any quantity of position values between 0 and 1 are used as input. The values are arranged randomly and there can be several million. To generate artificial databases, we recommend using MetaG-MetagenomicDatabaseGenerator.

The input files could look like the following:

   ...
   0.8632454772612163
   0.4474359764929482
   0.5169626625910273
   0.9848607471139751
   0.2062112094646345
   ...