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55 stars written in Java
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Load balancer API

Java 113 36 Updated Apr 19, 2024

🌺 reference-free transcriptome assembly for short and long reads

Java 107 9 Updated Jan 28, 2024

GenomeWarp translates genetic variants from one genome assembly version to another.

Java 97 21 Updated Jun 28, 2023

Ruby implementation of noncriptographic hash Murmur3 (both native and pure ruby)

Java 83 13 Updated Jan 5, 2023

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

Java 80 11 Updated Apr 1, 2024

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

Java 59 30 Updated Dec 21, 2022

SeqMonk NGS visualisation and analysis tool

Java 50 9 Updated Oct 2, 2025

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

Java 45 14 Updated Feb 17, 2021

Mapped QC analysis program

Java 44 8 Updated May 16, 2018

Runs the bellman-ford algorithm against bitcoin exchanges (currently Btc-e.com) to detect arbitrageable trade cycles.

Java 42 16 Updated Nov 20, 2015

Web based Registry platform for managing synthetic biological parts

Java 42 24 Updated May 16, 2024
Java 24 2 Updated Aug 17, 2016

The Nextflow language server

Java 24 4 Updated Nov 3, 2025

A Cytoscape app for importing KGML(KEGG pathway XML)

Java 24 10 Updated Mar 8, 2025

Sketch phylogenetic trees and networks

Java 23 Updated Nov 6, 2025

Biorepository application for tracking biospecimens.

Java 23 15 Updated Jun 9, 2024

VIGOR4

Java 21 13 Updated Aug 15, 2025

JTrek - a real-time space combat simulator played via telnet session

Java 18 5 Updated Nov 3, 2013

bacterial genome annotation system

Java 13 7 Updated Dec 11, 2014

A dotplot application for DNA/RNA sequence

Java 11 1 Updated Nov 28, 2022

Tn-seq Explorer allows users to explore and analyze Tn-seq data for prokaryotic (bacterial or archaeal) genomes. It implements two alternative methods for identification of essential genes and prov…

Java 7 2 Updated May 7, 2017

A new version of the pipeline based on CASAVA 1.8

Java 4 1 Updated Dec 20, 2011

Android Application to calculate optimal parameters for popular tools and kits available for DNA sequencing projects.

Java 3 1 Updated Jun 20, 2017
Java 2 Updated Mar 5, 2012

GA4GH plugin for Nextflow

Java 2 2 Updated Apr 16, 2025