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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SNP detection between 2 mouse strains

Discovering SNPs between 2 inbred mouse strains has been tested using the discoSNP strategy. Unlike many other approaches, discoSNP does not require a reference genome. The method is simply based on analyzing a de-Bruijn graph built from raw sequencing datasets.In this experimentation, two 100bp read datasets, representing 2.88 billions of…

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