Annotation Summary

Version: v0.0.1

What to use it for?

The Annotation Summary can be used to give you an excellent overview over your data. It will compare your DIAMOND-Megan6-Pipeline annotated metagenomic data to annotated metagenomic data from MG-Rast.

Prerequisites

This program is written Python and requires Python 3.6+. Furthermore, the following packages are required:

setuptools~=49.6.0
pandas~=1.2.4
matplotlib~=3.4.1
numpy~=1.19.2
scipy~=1.6.2

Options

Several Options are available. For some of them a stable internet connection is required.

MGM_ID

-id MGM_ID, --mgm_id MGM_ID

This option can be used when no MG-Rast ID is locally available. If included, it will download the necessary annotation files from the website, directly. The ID should be same as the one that was imported into Megan (The names must not be the same but the metagenomes should be). Note: This step might take a while due to very slow downloading speed of the Website.

Also, the -id option has a higher priority than -c or -k which are explained in more detail further below.

Output

-o OUTPUT, --output OUTPUT

The Path and file name to save the output to. Output will be a summary csv file comparing all annotations with each other. Also, graphics will be saved to the output path.

MEGAN_COG

-m_c MEGAN_COG, --megan_cog MEGAN_COG

Use this to import your exported Megan6 file. Export the required file from Megan6 by opening the EGGNOG viewer in the main panel. From there, uncollapse the annotation tree (Top-Panel => Tree => Uncollapse All) and select all nodes and leaves (Ctrl/Cmd + a). From the Top-Panel, choose File and move the cursor to Export and click on Text (CSV) Format. Export eggnogName_to_count and separator comma. The file that is then exported can be used for the analysis.

MEGAN_KEGG

-m_k MEGAN_KEGG, --megan_kegg MEGAN_KEGG

Use this to import your exported Megan6 file. Export the required file from Megan6 by opening the KEGG viewer in the main panel. From there, uncollapse the annotation tree (Top-Panel => Tree => Uncollapse All) and select all nodes and leaves (Ctrl/Cmd + a). From the Top-Panel, choose File and move the cursor to Export and click on Text (CSV) Format. Export eggnogName_to_count and separator comma. The file that is then exported can be used for the analysis.

NOTE: It is possible to analyze both, COG and KEGG in the same run.

MG-Rast COG

-c COG [COG ...], --cog COG [COG ...]

Include this option with all functional COG files that can be downloaded from MG-Rast (for a metagenome). If not locally available, provide the MG-Rast ID (mgm...) with this flag to download it similar to the -id option.

Note: If both, -id and -c are included, then -id is treated with a higher priority.

MG-Rast KEGG

-k KEGG [KEGG ...], --kegg KEGG [KEGG ...]

Include this option with all functional KEGG files that can be downloaded from MG-Rast (for a metagenome). If not locally available, provide the MG-Rast ID (mgm...) with this flag to download it similar to the -id option.

Note: If both, -id and -k are included, then -id is treated with a higher priority.