BioKotlin supports nucleotide and protein sequence manipulation, fast sequence IO, alignment, motif, pathway support.
BioKotlin leverages the performance and type safety of the JVM languages with ease of Python like scripting. Because the Kotlin language is compiled, it can be many times faster for certain applications than scripting languages. Because it uses the JVM, we expect high interoperability with GATK, SamTools HTSJDK, BioJava, TASSEL for GWAS and Genome Wide Prediction, and the PHG - the pangenome representation. Additionally, since we have mimicked the beautiful API of BioPython, we expect fast and efficient interoperability with BioPython through GraalVM.
You can follow our current progress at our GitHub Page
- Main website for BioKotlin
- Getting started
- Tutorials
- API reference (also on javadoc.io)
- Coming from BioPython?
- Benchmarks
The website is built from docs/ in this repository and deployed to
GitHub Pages on every push to master. See website/README.md
to build and preview it locally.
-
JupyterLab with Kotlin
- Install the Kotlin kernel for JupyterLab
- Add the following to your JupyterLab configuration file:
- %use biokotlin
-
Kotlin Script
- Add the following to your Kotlin script (.main.kts) file:
- @file:DependsOn("org.biokotlin:biokotlin:1.0.0")
-
Maven Central Dependency (i.e. pom.xml, build.gradle.kts)
-
Installable Tar File from Biokotlin Tools
- Download the latest tar file from (https://github.com/maize-genetics/biokotlin-tools/releases)