Toolchest runs computational biology software in the cloud with just a few lines of code. You can call Toolchest from anywhere Python or R runs, using input files located on your computer or S3.

Running one of our favorite computational biology tools – Kraken 2 – looks like:

import toolchest_client as toolchest
toolchest.set_key("YOUR_KEY")

toolchest.kraken2(
    tool_args="--minimum-base-quality 25",
    inputs="s3://toolchest-demo-data/SRR16201572_R1.fastq",
    output_path="./",
)

library(toolchest)
toolchest$set_key("YOUR_KEY")

toolchest$kraken2(
    tool_args = "--minimum-base-quality 25",
    inputs = "s3://toolchest-demo-data/SRR16201572_R1.fastq",
    output_path = "./"
)

🔧 Tools

Toolchest currently supports the following tools:

AlphaFold
Bowtie 2
Clustal Omega
Diamond
Kraken 2
RAPSearch2
STAR
Unicycler
...and more! Shoot us an email if you want to use software that isn't listed here.

📖 User Guide

Installation

Getting Started

Tutorials

If you're looking for supported databases or supported tool arguments, check out the tool-specific page (e.g. Kraken 2) – these are different for every tool.

📦 Client Packages

Toolchest offers a Python package and an R package.

Our client packages are open-source! Check out our GitHub repos here:

Toolchest Python client

Toolchest R client

💬 Contact us

If anything comes up, we'd love to talk! Shoot us an email at [email protected].