Yet Another Metagenome Binner
Project description
pyYAMB
pyYAMB is an implementation of YAMB (Yet another metagenome binner) on Python (>=3.8). Originally YAMB was described in the preprint https://www.biorxiv.org/content/10.1101/521286.abstract and it's main point is the use of tSNE and HDBSCAN to process tetramer frequencies and coverage depth of metagenome fragments. pyYAMB strives for parallel computing wherever possible, currently coverage depth extraction is single threaded and takes the most time.
pyYAMB data processing includes
- contig filtering and fragmentation
- read mapping with minimap2
- mapping files processing and coverage depth extraction with pysam
- k-mer (by default tetramer) frequency calculation
- data dimensions reduction with tSNE
- data clustering with HDBSCAN
- writing bins to FASTA
Possible features in far future
- read processing
- metagenome assembly
- bin QC
How to start
Warning! pyYAMB now is in alpha-testing and may be unstable, use it at Your own risk.
Installation
Conda
pyYAMB is available at Anaconda and may be installed with all dependencies:
conda install -c laxeye pyyamb
PyPI
pyYAMB is available at PyPI and may be installed with:
pip install pyYAMB
Also yo need to install dependencies
GitHub
Another way (not recommended) is to clone the repository
git clone https://github.com/laxeye/pyYAMB.git
or gh repo clone laxeye/pyYAMB
and run
python setup.py install
It installs pyYAMB and python libraries. Problems may appear with hdbscan module and cython. Just reinstall hdbscan using pip install hdbscan
and try again python setup.py install
.
Dependencies
If you installed pyYAMB from PyPI or GitHub, you need to install dependencies: minimap2 and samtools (e.g. using conda).
conda install -c bioconda minimap2 "samtools>=1.10"
Usage
pyYAMB entry point is the all-in-one command pyyamb
. pyYAMB has two dozens of arguments, their description is available after running pyyamb -h
You may start from metagenome assembly and processed (quality trimmed etc.) reads, e.g.:
pyyamb --task all -1 Sample_1.R1.fastq.gz Sample_2.R1.fastq.gz -2 Sample_1.R2.fastq.gz Sample_2.R2.fastq.gz -i assembly.fasta -o results/will/be/here --threads 8
After completion bins could be found in bins subfolder in output folder. "-1" bin collects unbinned sequences.
Results and benchmarks
pyYAMB will be tested on CAMI dataset soon. YAMB showed quality compared with CONCOCT binner (see the preprint for details).
References
Van Der Maaten, L. (2014). Accelerating t-SNE using tree-based algorithms. The Journal of Machine Learning Research, 15(1), 3221-3245.
Campello, R. J., Moulavi, D., & Sander, J. (2013, April). Density-based clustering based on hierarchical density estimates. In Pacific-Asia conference on knowledge discovery and data mining (pp. 160-172). Springer, Berlin, Heidelberg.
Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. https://dx.doi.org/10.1093/bioinformatics/bty191
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome research, 25(7), 1043-1055. https://dx.doi.org/10.1101/gr.186072.114
Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., ... & De Hoon, M. J. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422-1423. https://doi.org/10.1093/bioinformatics/btp163
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