MG-TK

Introduction

MG-TK is a pipeline developed to

• Assemble metagenomes, profile miTags, profile functions, profile taxonomy, build MAGs (metagenomic asssembled genomes) using a variety of approaches (MG-TK.pl)
• Build a gene catalog based on these assemblies and predicted genes, build abundance matrices from these and annotate the genes functionally (secScripts/geneCat.pl)
• Merge MAGs into MGS (metagenomic species), build inter- and intra-speciies phylogenies (secScripts/MGS.pl)
• Additional functionalities are available, such as building phylogenetic tree automatically for many genomes and calcualting population genetic statistics on these (secScripts/phylo/buildTree5.pl)

MG-TK is implemented in Perl, C++ and uses R and python scripts.

Author: Falk Hildebrand Falk.Hildebrand@gmail.com

Detailed information

• Installing MG-TK
  • I/O considerations
  • Known Issues
• MG-TK manual
  • MG-TK.pl flags
  • Genecat.pl flags
  • MGS.pl flags
  • buildTree5.pl flags
• Outputs
  • Abundance matrices
  • Gene function & MAG/MGS gene content
• Running MG-TK
  • Temporary and output files
  • Mapping file
  • Additional usage scenarios
    • map2tar mode
    • Building phylogenetic trees with MG-TK
• Examples
  • MG-TK metagenomic assembly and gene catalog
  • Assembly-independent MG-TK mode
  • Hybrid assemblies
• FAQ

License, citations etc

Expand section

Used software

plenty.. please refer to helpers/install/*.yml for software that is available on Conda.

Other software used that was adapted and/or developed specifically for MG-TK (all implemented in C++):

• sdm, LCA: for 1) read qual filtering 2) least common ancestor calculations in tax assignments. Both are part of our amplicons sequencing pipeline LotuS2
• clusterMAGs: cluster MAGs into MGS (metagenomic species) based on conserved marker genes
• camopy2: canopy clustering of gene catalogues, a much more efficient implementation of the original algorithm
• MSAfix: fixes frameshifts in MSA that sometimes occur, important for high senstive intraspecific phylogenies
• rdCover: calculates read coverage of genes, genomes etc based on mappings.

Citing MG-TK

Please cite MG-TK with:

• Assembly mode: Hildebrand, F. et al. Antibiotics-induced monodominance of a novel gut bacterial order. Gut 68, 1781–1790 (2019).
• Strain mode: Hildebrand, F. et al. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host & Microbe 29, 1167-1176.e9 (2021).
• Assembly-independent mode: Bahram, M. et al. Metagenomic assessment of the global diversity and distribution of bacteria and fungi. Environmental Microbiology 23, 316–326 (2021).
• sdm, LCA: Özkurt, E. et al. Microbiome (2022).

Falk Hildebrand Falk.Hildebrand@gmail.com

License

Copyright (c) 2017-2024 Falk Hildebrand

MG-TK is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

MG-TK is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the file LICENSE for more details.

You should have received a copy of the GNU General Public License along with the source code. If not, see http://www.gnu.org/licenses/.