GATB used by NCBI for Gnomon

NCBI uses parts of the GATB-Core library in the Gnomon eukaryotic gene prediction tool. This can be reviewed in the De Bruijn graph implementation of Gnomon available in the NCBI c++ Toolkit, see here.

Continue reading

GATB Programming Day – Spring 2017

Are you interested in learning how to make high-performance software tools to decypher reads data? Are you a little familiar with C++ programming? Are you happy to come to Spain during Spring 2017? Ok, this event if fully made for you: The Genscale team will hold a GATB Special Session during…

Continue reading

New GATB programming tutorial

We have created a brand new tutorial to help you learning the GATB-Core API. It provides you with a 3-step learning trail: Rookie, Expert and Advanced. All tutorial trails contain a little piece of theory and a c++ code snippet… that can be executed online, without the need (for you)…

Continue reading

GATB programming day – Fall 2016

Are you interested in learning how to create high-performance NGS data analysis tools? Are you familiar with C++ programming and can you speak English? If so, Ok, well done ;). This event is for you: The GATB programming day: learn the basics of high-performance NGS data processing using the GATB-Core library. This second edition…

Continue reading

MindTheGap new release !

MindTheGap v2.0.0 has just been released ! In fact, this is the first release with the GATB library. After a long period with few developments (publication in 2014), the whole code of MindTheGap was refactored to use the GATB library. Therefore MindTheGap became faster and easier to use. In addition,…

Continue reading

GATB programming day: summary

On June 15th, 2016, our training room at Inria Rennes welcomed 15 people (researchers, engineers and PhD students in bioinformatics) to attend to our first GATB programming day. Quite a success since our room was fully occupied! During that day, we got into the following topics: a theoretical introducton to…

Continue reading

GATB-core 1.2.0 released

Get it on Github Release notes Assembly-inspired de Bruijn graph simplifications // removes tips, bubbles and erroneous connections, // similar to some of the algorithms implemented in the SPAdes assembler graph.simplify(); Faster graph traversal can be activated using a single command. // allocates 1 byte/node to precompute adjacency for each…

Continue reading