Notable open source bioinformatics projects written in Java?

Question

[kam.stratos]

I'm a Computer Science undergraduate writing my thesis which is about analyzing open source bioinformatics projects and extracting standalone modules. I need those projects to be written in Java and preferably be stable or mature. So far I've found a bunch of projects via SourceForge and I was wondering if there are any notable ones that are not hosted there. A different repository that has a bioinformatics category would be helpful too.

Here's a list of the most promising projects I have so far:

• Jenetics
• JGap
• Jmol
• Juicebox
• Picard
• RDP Classifier
• Shim
• Tassel
• The Chemistry Development Kit
• Toxfree
• TreeView
• VarScan

Thanks in advance.

[dariober]

I think SourceForge is going out of fashion and it's being overcome by Github.

[kam.stratos]

I agree, but it does have a "bioinformatics" category and supports filtering based on project maturity. Thanks for your suggestions below.

Answer 1

[Pierre Lindenbaum]

• htsjdk
• gatk
• igv
• haploview

... Edit and using the seqanswer wiki.

[kam.stratos]

That edit is a thread killer. Thanks!

Answer 2

[GenoMax]

• BBMap
• FastQC

Answer 3

[dariober]

• Biojava
• Seqmonk
• GSEA

Answer 4

[Philipp Bayer]

• MHAP (part of Canu long read assembler)
• The server part of QTLNetMiner is written in Java https://github.com/KeywanHP/QTLNetMiner
• PacBio's SMRT Analysis is partially written in Java, but I don't know whether it fits your requisites, it seems to be open source but I can't find a license
• JAligner
• Jalview

Answer 5

[Dan D]

JEnsembl is a JAVA API for Ensembl.

Contrail and Cloudbase are assemblers. The latter got some new life when an enterprising programmer retooled it for GPUs.

Answer 6

[mkulecka]

• Archaeopteryx
• Cytoscape