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…
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…
A new discoSnp++ available. It fixes a kissread bug, that affected slightly coverage counting. Check out the dedicated web page: https://github.com/GATB/DiscoSnp
*Event is now fully booked! Please get in touch with us to pre-book for a future session.* The first GATB programming day will be held at Inria Rennes on coming June 15th. You are interested in learning how to create high-performance NGS data analysis tool? You have good skills in…
A Github repository has been setup to provide a convenient access to GATB-Core softwares. It can be used to get instant access to latest sources as well as official releases. See https://github.com/GATB/gatb-core.
GATB assembly pipeline entered the 1st CAMI Challenge (Critical Assessment of Metagenome Interpretation). Follow this link to read results evaluation
Our new read compression software Leon has been published in BMC Bioinformatics : http://www.biomedcentral.com/1471-2105/16/288. Leon is a software to compress Next Generation Sequencing data. It can compress Fasta or Fastq format. The method does not require any reference genome, instead a reference is built de novo from the set of…
A new release of GATB-CORE is now available. This is a maintenance release that includes several fixes. More here.
The new version of the GATB-CORE library 1.0.6 is now available. This version provides: speed up from x2 to x4 for kmer counting and graph construction phases (optimizations based on minimizers and improved Bloom filters). GATB’s k-mer counter has been improved using techniques from KMC2, to achieve competitive running times…
The GATB team was at ISCB Latin America 2014 in Belo Horizonte, Brazil (October 28-30) A presentation of GATB was made and a workshop was proposed at UFMG (you can find the slides here).
