bioluminescence

Bioluminescence is a java library for facilitating de novo genome assembly in the context of reads sampled from a single highly-polymorphic diploid individual. Bioluminescence implements a novel algorithm which uses an artificial neural network to classify contigs in a genome assembly as haplotype-specific or not-haplotype-specific. It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. Initial results using this technique have dramatically improved de novo asseblies of such data. The implementation provided here remains partial, and under daily development, and is released as a daily "snapshot" as opposed to a static version.