Tools for detecting DNA modifications from single molecule, real-time (SMRT®) sequencing data. This tool implements the P_ModificationDetection module in SMRT® Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol. Researchers interested in understanding or extending the modification detection algorithms can use these tools as a starting point.

Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and the other holding k-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.

This is the GNU D compiler, which compiles D on platforms supported by gcc. It uses the gcc backend to generate optimised code.

Async is a modern concurrency framework for Ruby. It implements the reactor pattern, providing both non-blocking I/O and timer events.

Bring in livereload.js into handy Rack middleware.

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.