README

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

BioKotlin Links

• Main website for BioKotlin
• Documentation (API)

How to Use

• 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)

  • https://mvnrepository.com/artifact/org.biokotlin/biokotlin

• Installable Tar File from Biokotlin Tools

  • Download the latest tar file from (https://github.com/maize-genetics/biokotlin-tools/releases)

Who do I talk to?

• Discussion Page
• Issues Page