Main module
link
: linking MAGs with 16S rRNA marker genesSupplementary modules
MarkerMAG is implemented in python3, It has been tested on Linux and MacOS, but NOT on Windows.
A Conda package that automatically installs MarkerMAG's third-party dependencies (except Usearch :warning:) is now available. Please note that you'll need to install Usearch on your own as it's not available in Conda due to license issue.
conda create -n MarkerMAG_env -c bioconda MarkerMAG
conda activate MarkerMAG_env
conda deactivate
It can also be installed with pip. Software dependencies need to be in your system path in this case.
Dependencies for the link
module include
BLAST+,
Barrnap,
seqtk,
Bowtie2,
Samtools,
HMMER,
metaSPAdes and
Usearch.
Dependencies for the supplementary modules are provided in their corresponding manual page.
pip3 install MarkerMAG
pip3 install --upgrade MarkerMAG
Here are some example commands for UNSW Katana users.
:warning: If you clone the repository directly off GitHub you might end up with a version that is still under development.
MarkerMAG’s input consists of
matam_16s
module) :warning: MarkerMAG is designed to work with paired short-read data (i.e. Illumina). It assumes the id of reads in pair in the format of XXXX.1
and XXXX.2
. The only difference is the last character.
You can rename your reads with MarkerMAG's rename_reads
module (manual).
Although you can use your preferred tool to reconstruct 16S rRNA gene sequences from the metagenomic dataset,
MarkerMAG does have a supplementary module (matam_16s
) to reconstruct 16S rRNA genes.
Please refer to the manual here if you want to give it a go.
Link 16S rRNA gene sequences with MAGs (demo dataset):
MarkerMAG link -p Demo -r1 demo_R1.fasta -r2 demo_R2.fasta -marker demo_16S.fasta -mag demo_MAGs -x fa -t 12
Summary of identified linkages at genome level:
Marker | MAG | Linkage | Round |
---|---|---|---|
matam_16S_7 | MAG_6 | 181 | Rd1 |
matam_16S_12 | MAG_9 | 102 | Rd1 |
matam_16S_6 | MAG_59 | 55 | Rd2 |
Summary of identified linkages at contig level (with figure):
Marker___MAG (linkages) | Contig | Round_1 | Round_2 |
---|---|---|---|
matam_16S_7___MAG_6(181) | Contig_1799 | 176 | 0 |
matam_16S_7___MAG_6(181) | Contig_1044 | 5 | 0 |
matam_16S_12___MAG_9(102) | Contig_840 | 102 | 0 |
matam_16S_6___MAG_59(39) | Contig_171 | 0 | 55 |
Copy number of linked 16S rRNA genes.
Visualization of individual linkage.
MarkerMAG supports the visualization of identified linkages (needs Tablet). Output files for visualization (example) can be found in the [Prefix]_linkage_visualization_rd1/2 folders. You can visualize how the linking reads are aligned to MAG contig and 16S rRNA gene by double-clicking the corresponding ".tablet" file. Fifty Ns are added between the linked MAG contig and 16S rRNA gene.
*If you saw error message from Tablet that says input files format can not be understood, please refer to here for a potential solution.