PhD Student, GenScale team, IRISA (UMR CNRS 6074), Rennes, FRANCE
Using Short Read Connector (SRC)
SRC (short read connector) is an alignment-free tool dedicated to the detection of similar reads, based on their k-mer content. Importantly, SRC has been originally designed to scale up to highly voluminous reads data sets, such as those encountered in meta-genomics experiments, by embedding an original and lightwheight implementation of a minimal perfect hash function. At the current time SRC methods and data structure are presented in two papers  and . Quite naturally, a typical SRC's use case can be meta-genomic analysis in an ecology context. We are currently going deeper in this topic with the team "Analyse des donnees a haut debit en genomique" in MNHN, Paris. Lately we also investigate its potential in the recruitement of Third Generation Sequencing reads.
SRC comes as two different tools, Short Read Connector Counter and Short Read Connector Linker that are described on our github, as well as the installation and starting commands. If you have any questions on its applications or whether it would be suitable for your own project, I'd be happy to answer.