The rapid evolution of DNA sequencing technologies over the past 20 years has made it possible to generate enormous amounts of data, and has subsequently spurred the development of computational tools needed to assemble complete genomes and to analyze genomic, transcriptomic and proteomic data. The GSC collaborates with and supports research by the wider research community. We have an extensive collection of software packages developed in-house available for download here and through GitHub.


Visualize comparative genomic data such as alignments, conservation, homology, synteny and other positional n-tuples in an attractive and informative circular layout


DIDA is a novel framework that performs the large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes


DiscoverySpace is a graphical software application that intends to free the biologist from the micro-level, syntactic detail of the underlying data structures to concentrate on the "big picture" and the meaning of experimental results


GraphNER is a named entity recognizer that uses graph propagation and improves BANNER and BANNER-ChemDNER systems. Data is available for gene mention detection task


c(K)LEavage site Analysis of Transcriptomes (KLEAT) identifies 3' UTR ends of transcripts in de novo RNA-Seq assemblies


LaneRuler will identify lanes in a gel image. The core module is a command line C program, whose result can be reviewed and corrected using a Java interface


LongStitch is a de novo genome assembly correction and scaffolding pipeline. LongStitch runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long).


Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering Publication


THOR, the Targeted High-throughput Ortholog Reconstructor, is a Java application designed to assemble target genomic sequence orthologs in low-coverage genomes
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