From the Caffe website: Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by Berkeley AI Research ( BAIR ) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license .
ABySS is a de novo, parallel, paired-end genomic sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. To assemble transcriptome data, consider the related program trans-abyss. Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
From the Pilon documentation: "Pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies as well as call variants."
R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.