GATB programming day – Summer 2016

*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…

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GATB-core on github

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.

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CAMI Challenge

GATB assembly pipeline entered the 1st CAMI Challenge (Critical Assessment of Metagenome Interpretation). Follow this link to read results evaluation

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Leon published in BMC Bioinformatics

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…

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New GATB-CORE version 1.0.6

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…

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DSK vs. Kanalyze

Results reported in the paper KAnalyze: A Fast Versatile Pipelined K-mer Toolkit in Bioinformatics about DSK don’t seem to fit the reality. Taking the same datasets, we run DSK and Kanalyze on our machines. The following table summarizes our experiments. KAnalyze DSK NA18580 1.5 M reads – 453 Mbp 201…

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