This is the test repo for anchorage assembly method. All evaluations were performed on an intel iMac.
Our experiments involve those tools.
| Tool | Version | Description | Reference |
|---|---|---|---|
| Anchorage | Assembly tool | [github] [publication] | |
| SPAdes | v3.15.5 | Assembly tool | [github] [publication] |
| MEGAHIT | v1.2.9 | Assembly tool | [github] [publication] |
| Polyester | 1.38.0 | Read simulator | [github] [publication] |
| QUAST | v5.2.0 | Quality Assessment Tool for Genome Assemblies | [github] [publication] |
Also, we used seaborn and pandas python packages to plot figures.
Most tools can be installed and managed using conda. We manually compiled and installed MEGAHIT as described here. Users should make all related tools can be called directly from $PATH. Also, anchorage should be installed in the programs directory and its dependencies should be properly installed.
cd programs
git clone https://github.com/Shao-Group/anchorage.git
# install anchorage dependencies
conda env create -f programs/anchorage/src/python/environment.yml
conda activate anchorageAfter all related tools are installed. Run sh scripts/main.sh to reproduce results.
This repo is under BSD 3-Clause License. Some of the scripts is based on code from LoopCore repo which is also under BSD 3-Clause License (LoopCore license).