GATB published in Bioinformatics
E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier (2014) GATB: Genome Assembly & Analysis Tool Box Bioinformatics, Bioinformatics, 30(20):2959-2961 link to article
GATB at BIO-IT 2014
The GATB project will be present at Bio-IT 2014 in Boston (April 29 – May 1) You can have a look here at the poster that will be presented then.
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…
Assembling the raspberry genome on a Raspberry Pi computer
GenScale has managed to assemble the raspberry genome on . . . the eponymous Raspberry Pi, a mini-computer with only 512MB of RAM. The goal was essentially to demonstrate the dramatically low memory footprint of GATB. Read the article. Some technical details We are very grateful to Joshua Udall from…
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…
GATB-CORE is available !
The GATB-CORE library is now available and can be downloaded here. You can also have a look on this HelloWorld page that will provide the minimal material required to use the GATB-CORE library.
Minia on Raspberry PI
In order to demonstrate the low memory footprint of Minia, a read contiger built from the GATB-core library, we experienced the implementation of this software on the Raspberry Pi computer. The Raspberry Pi is a credit-card-sized single-board computer including an ARM1176JZF-S 700 MHz processor and 512 megabytes of RAM. Operating…
Assembling the raspberry genome on a Raspberry Pi computer
Read the article.
