What is Toolchest?

Introduction to Toolchest

Toolchest is a library that offloads execution of bioinformatics software to the cloud. With seamless setup and automatic cloud deploys, Toolchest lowers time-to-production, increases reproducibility, and eliminates time spent setting up bioinformatics packages and managing cloud infrastructure.

If you're familiar with Toolchest, feel free to skip to the quick start.

Why Toolchest?

Toolchest provides an easy to install, fast to run, and seamless way to scale bioinformatics software in the cloud to maximize the speed of research for you and your team. We also optimize Toolchest heavily to reduce your cloud costs, which can save teams >80% of what they'd otherwise spend on cloud computing.

To work so seamlessly, we make the same open-source tools you already use – like AlphaFold, Bowtie 2, or STAR – available on top of gold-standard tooling like AWS and Docker. Everything is automatically configured and deployed from Toolchest in Python, R, or the command line.

For Researchers

If you analyze biological data, Toolchest packages bioinformatics tools so you can run them in the cloud without leaving the way you already analyze data (e.g. the command line, R Studio, a Jupyter notebook, a Python script, Snakemake, Nextflow etc). You can analyze a terabyte of data in the same way you analyze a megabyte of data – without worrying if you have enough computing power or RAM. Say goodbye to choosing between months learning something unrelated to your research vs. waiting for a team member to deploy your pipeline.

For Infrastructure Engineers

If you work on building infrastructure for bioinformatics pipelines, Toolchest gives you a way to use the best practices in data engineering without diving deeply into bioinformatics-specific workflow managers. Instead of relying on domain specific workflow managers like Nextflow, Snakemake, or CWL, you can use Toolchest to wrap the bio-specific heavy lifting and use gold-standard workflow managers like Airflow, Dagster, or Prefect – used by data engineering teams at Apple, Amazon, DoorDash, Figma, Scale AI, and others. You can finally put managing bioinformatics-specific workflow managers in the rearview mirror.

For Execs

People who build bioinformatics pipelines have a unicorn skillset. Toolchest turns more team members into unicorns: your researchers run in the cloud as if you hired them from AWS, and your infrastructure engineers build scalable bioinformatics pipelines while keeping them maintainable by your researchers. This means your team can set up a production pipeline in days instead of months, and maintainence is easier. Toolchest also uses AWS resources efficiently: your baseline spend on cloud computing can be $0, increasing only as more data is analyzed.


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