separating strains in metagenomic assemblies using ILP
WARNING strainMiner is not actively supported. Please go to HairSplitter to see an up-to-date strain separator. The strainMiner presented here nonetheless is the only one implementing ILP, and thus can perform slightly better than HairSplitter in some cases.
You will need to have installed in your PATH (for example in a conda environment):
- minimap2
- samtools
- racon
Additionally, you wil need to have installed:
- pysam
- pandas
- sklearn
- gurobipy with a valid gurobi license
Additionally, you will need to have installed pysam, and gurobipy, to use with a valid gurobi license.
To use your gurobi license, modify lines 27 to 31 of strainminer.py
Then download and build strainMiner:
git clone https://github.com/RolandFaure/strainMiner.git
cd strainMiner
mkdir build
cd build
cmake ..
make
usage: strainminer.py [-h] -a ASSEMBLY -b BAM -r READS [-e ERROR_RATE] -o OUT [--window WINDOW]
optional arguments:
-h, --help show this help message and exit
-a ASSEMBLY, --assembly ASSEMBLY
Assembly file in gfa format
-b BAM, --bam BAM Alignment file in BAM format
-r READS, --reads READS
-e ERROR_RATE, --error_rate ERROR_RATE
Estimation of the error rate of the data
-o OUT, --out-folder OUT
Name of the output folder
--window WINDOW Size of window to perform read separation (must be at least twice shorter than average read length) [5000]
A pre-print is available on HAL, https://inria.hal.science/hal-04349675.
Tam Minh Khac Truong developped and implemented the read separation module, under the supervision of Roland Faure and Rumen Andonov. Roland Faure integrated the module into the HairSplitter pipeline to produce a complete software.