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BASALT is a versatile toolkit that recovers, compares and optimizes MAGs across a series of assemblies assembled from short-read, long-read or hybrid strategies. Firstly, BASALT uses high-throughput assembly methods to automatically assemble/co-assemble multiple files in parallel to reduce the manual input; Next, BASALT incorporates self-designed algorithms which automates the separation of redundant bins to elongate and refine best bins and improve contiguity; Further, BASALT facilitates state-of-art refinement tools using third-generation sequencing data to calibrate assembled bins and complement genome gaps that unable to be recalled from bins; Lastly, BASALT is an open frame toolkit that allows multiple integration of bioinformatic tools, which can optimize a wide range of datasets from various of assembly and binning software.

The resource requirements for this pipeline will be based on the amount of data being processed. However, due to large memory requirements of many softwares used (e.g. SPAdes), 8+ cores and 125GB+ RAM are recommended. BASALT officially supports only Linux x64 systems.

As there are many required dependencies needed to install, we highly recommend that you install and manage BASALT with conda. Once you have Miniconda or Anaconda installed, create a conda environment and install the BASALT within the specific environment.

1 Download this basalt_env.yml.

2 (Optional) You can also use mirrors to increase the download speed of BASALT dependent software. For example,if you are in China, you can do this:

site=https://mirrors.tuna.tsinghua.edu.cn/anaconda
conda config --add channels ${site}/pkgs/free/ 
conda config --add channels ${site}/pkgs/main/
conda config --add channels ${site}/cloud/conda-forge/
conda config --add channels ${site}/cloud/bioconda/ 

3 Make a new conda environment to install and manage all dependancies:

conda env create -n BASALT --file basalt_env.yml

The step 3 will take a while.

4 Download this BASALT.zip. Then upload this file to your Linux directory.

unzip BASALT.zip
chmod -R 777 BASALT

Move BASALT files to your conda BASALT environment. In general, your conda BASALT environment is located in the subdirectory envs of the conda installation (e.g. /home/anaconda2/envs/).

mv BASALT/* /home/anaconda2/envs/BASALT/bin

We have also prepared sample files (see Sample_data.tar.gz) for testing whether the BASALT script can be successfully performed and the bins can be generated. The sample files contain two assembly files and two fastq datasets. Please refer to the tutorial for how to execute the BASALT scripts.

Yu, K., Qiu, Z., Mu, R., Qiao, X., Zhang, L., Lian, C. A., ... & Zhuang, W. (2021). Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT. bioRxiv.