TMarSel 0.1.1

select gene families as markers for microbial phylogenomics

TMarSel

TMarSel is a tool for a Tailored Selection of gene families as Markers for microbial phylogenomics.

Table of contents

• Inputs
• Outputs
• Installation
• Basic usage
• Examples
• Citation

Flags

• -h Display help message.
• -i [required] Either a single annotation of ORFs into gene families file OR a direcotry containing multiple annotation files. File(s) contains three columns: orf|bit_score|gene_family.
• -o [required] Output directory to save the ORFs and statistics of each marker.
• -raw [required] IF input file(s) contain raw annotations from functional databases, which contains multiple columns depending on the database.
• -db [required] IF input contains the raw annotations set in -raw. Name of the database used for genome annotation (eggnog or kegg).
• -k Number of markers to select (default is 50).
• -min_markers Minimum number of markers per genome. Can be a percentage or a number (default is 1). Genomes with fewer markers than the indicated value are discarded.
• -th Threshold for filtering copies of each gene family per genome (default is 1.0) Retain the ORFs within -th of the maximum bit score for each gene family and genome. Lower values (e.g. 0.0) retains all ORFs, whereas higher values (e.g. 1.0) retains only the ORF with the highest bit score.
• -p Exponent of the power mean (cost function) used to select markers (default is 0.0). We recommend not changing this value unless you are familiar with the method. Default value yields the optimal combination of markers.

Outputs

1. k files containing the ORFs, genome and file of origin for each marker (see below). Files are saved to ./output_dir/orfs.

orf	genome	file
G000006605_1748	G000006605	kofamscan_wol2_example.tsv
G000006725_378	G000006725	kofamscan_wol2_example.tsv
...	...	...

2. Statistics. Files are saved to ./output_dir/statistics

• Number of markers per genome (see below). A given marker can contain more than one ORF per genome, therefore we provide the number of different markers (k) and the total number of markers. The details column is ; separated. Each item indicates the marker name and the number of ORFs (i.e. copies) in the genome.

genome	number_of_different_markers	total_number of markers	details
G000006605	10	10	K01889:1;K01866:1; ...
G000006725	9	10	K02358:2;K01872:1; ...
...	...	...	...

• Number of genomes per marker (see below). We provide the number of genomes containing the marker. The details column contains the genome name and the number of ORFs of the marker.

marker	number_of_genomes	details
K01409	1509	G000093065:2;G900097235:2;G002074035:2; ...
K01866	1508	G900097235:2;G001941465:2;G000006605:1; ...

Installation

• pip

pip install TMarSel

Basic usage

 tmarsel -i input_file_or_dir -o output_dir

After installation, type tmarsel -h to learn all the options.

Examples

We provide multiple examples to showcase the usage of TMarSel. Data can be downloaded as explained in files.

1. Annotations of 1,510 genomes from the Web of Life 2 database

• EggNOG annotations contained in a single file with three columns orf|bit_score|gene_family. See annotation for formating the raw annotation files.

tmarsel \
    -i    data/wol2/emapper_wol2_example.tsv \
    -o    out/wol2 

• KEGG annotations contained in a single file with three columns orf|bit_score|gene_family. See annotation for formating the raw annotation files.

tmarsel \
    -i    data/wol2/kofamscan_wol2_example.tsv \
    -o    out/wol2 

2. Annotations of 793 metagenome-assembled genomes (MAGs) from the Earth Microbiome Project

• EggNOG annotations contained multiple files with three columns orf|bit_score|gene_family. See annotation for formating the raw annotation files.

tmarsel \
    -i data/emp/eggnog_format \
    -o        out/emp

• EggNOG annotations contained in multiple files with raw annotations.

tmarsel \
    -i data/emp/eggnog \
    -o        out/emp \
    -db          eggnog \
    -raw

• KEGG annotations contained in multiple files with three columns orf|bit_score|gene_family. See annotation for formating the raw annotation files.

tmarsel \
    -i data/emp/kegg_format \
    -o        out/emp

• KEGG annotations contained in multiple files with raw annotations.

tmarsel \
    -i data/emp/kegg \
    -o        out/emp \
    -db          kegg \
    -raw

Citation

The current version of TMarSel is described in

• x.x