Next GATB Programming day — July 2019 — Nantes (France)

A new GATB Programming Day is scheduled on July 1rst, 2019 in Nantes, France, the day before the french conference JOBIM. This training session provides bioinformatics developers with the basics of GATB-Core library to design and create high-performance software to process and analyze high throughput sequencing data. Please, follow this…

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GATB Programming day — April 2018 — Paris

A new GATB Programming Day is scheduled on April 18th, 2018 in Paris, France, the day before the international conference RECOMB-seq. This training session provides bioinformatics developers with the basics of GATB-Core library to design and create high-performance software to process and analyze sequencing read data. Please, follow this link…

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GATB Programming Day – Rennes

A new GATB Programming Day is scheduled on October 24th, 2017 in Rennes, France. This event takes place to provide bioinformatics developers with the basics of GATB-Core library to design and create high-performance software to process and analyze sequencing reads data. Please, follow this link to get all details concerning…

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GATB-Tools on Docker

We have released a new project: the GATB-Tools Docker Machine. This project is hosted on Github and provides you with the capability of using several GATB-Tools with a Docker Container. As of today, available GATB-Tools are: Simka DSK BLOOCOO MindTheGap Minia Short Read Connector DiscoSNP++ TakeABreak This Docker container can…

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GATB Tutorial at IBC, Montpellier

On June 16th, 2017, we conducted our 4th GATB Programming Day at IBC, Montpellier, France. We warmly thank Eric Rivals and his team for organizing the session in his lab, as well as all participants to come over Montpellier. Tutorial material (documents, sample source codes and test data) will remain…

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pyGATB speed test

A little test on counting nucleotides in the C.elegans genome is available on StackExchange: pyGATB is ranked second fastest tool. Tested tools are: bioawk, shell pipeline (grep + tr + grep), pure python, biopython, readfq and pyGATB. Top 3 fastest tools are as follows (real time value): grep/tr/wc: 0m 0.609s…

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GATB at Hackathon Inria

Paris, France, June 7th 2017 – the Genscale Team participated to the first event celebrating the “50 years anniversary” of Inria : “What will be our digital future in 2067”. Inria was born in 1967: we can look back in the past on what we did, but we should also…

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Xcode and GATB

To help new developers to start working with GATB-Core projects on OSX computers, we have setup this article to explain how to install and configure the Xcode IDE for that purpose. Among others, it shows how to use CMake (on which GATB projects rely) and Xcode in a very straightforward…

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pyGATB: Python wrapper for GATB

We have just released a Python 3 wrapper for the GATB-Core library: pyGATB. The current release of pyGATB gives access to the following GATB-Core components: Bank: the class that enables to load Fasta and Fastaq files Sequence: the class that holds a sequence (ID, letters, quality) Graph: the class that…

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