User: patrick.durand

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Posts by patrick.durand

<prev • 14 results • page 1 of 2 • next >
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PBSuite does not run within a Docker container
... Hello, I'm setting up a Docker image for the PBSuite software (https://sourceforge.net/projects/pb-jelly/ ). However, the software fails on its own test data set... I put everything available here (detailed description of the problem) : https://github.com/pgdurand/pbsuite-docker/issues/1 Any hel ...
assembly next-gen written 12 months ago by patrick.durand120
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Answer: A: BeeDeeM: the bioinformatics databank manager system
... A Docker support has been added to facilitate the use of BeeDeeM. [Read this][1]. [1]: https://github.com/pgdurand/BeeDeeM/tree/master/docker ...
written 19 months ago by patrick.durand120
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Tool: new release for GATB, the Genome Analysis Toolbox with de-Bruijn graph
... A new release of the [GATB-Core][1] library is now available for upload. A summary of GATB-Core 1.3.0 new features an updates is as follows: * A new graph object is introduced: GraphUnitigs, optimized to traverse unitigs but not to query individual kmers * A few graph API functions have been chan ...
tools next-gen gatb written 19 months ago by patrick.durand120
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Tool: BeeDeeM: the bioinformatics databank manager system
... The Bioinformatics Databank Manager System (*BeeDeeM*) is capable of installing on a local computing system major sequence databank file formats: Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta, Silva and BOLD. In addition to sequence data files, BeeDeeM can install major biological classif ...
blast uniprot tool genbank databank written 19 months ago by patrick.durand120
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News: GATB-Core Library Tutorial - Making efficient NGS data analysis softwares
... - Are you interested in learning how to make high-performance software tools to decypher reads data? - Are you a little familiar with C++ programming? - Are you happy to come to Spain during Spring 2017? Ok, this event if fully made for you: The [Genscale team][1] will hold a **GATB Special Sessi ...
news next-gen tutorial gatb tool written 19 months ago by patrick.durand120
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Comment: C: How to retrieve COSMIC variations using Ensembl REST API?
... Hi Ben, ok, got it, thanks. By the way, do you have any documentation that gives more insights on how to combine feature types with variant_set. E.g. if I use "feature=variation", what are the appropriate values for "variant_set" ? I cannot find that information from the "overlap" service web page, ...
written 21 months ago by patrick.durand120
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How to retrieve COSMIC variations using Ensembl REST API?
... I'm failing to retrieve Cosmic variations for some human genes using Ensembl API. Using a web browser with this link: http://www.ensembl.org/Homo_sapiens/Transcript/ProtVariations?db=core;g=ENSG00000141510;r=17:7661779-7687550;t=ENST00000617185 illustrates that Cosmic variations are available fo ...
ensembl api variation cosmic written 21 months ago by patrick.durand120 • updated 15 months ago by Biostar ♦♦ 20
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News: Workshop on making high-performance NGS data analysis softwares
... Hello, - Are you interested in learning how to make high-performance software tools to decypher reads data? - Are you a little familiar with C++ programming? - Are you happy to come to Spain during Spring 2017? Ok, this event if fully made for you: > [The Genscale Team][1] (Inria) will hold ...
software news next-gen gatb written 22 months ago by patrick.durand120
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Tutorial: New GATB-Core Tutorial: learn the Genome Analysis Tool Box... online
... The [GATB-Core][1] library is a free and open-source high performance tool providing efficient data structures and algorithms to decypher NGS reads by means of kmers, de Bruijn graphs, hash tables, etc. This library has already been used to design read correctors, assemblers, SNP callers, etc. In o ...
tutorial next-gen gatb written 23 months ago by patrick.durand120
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Tool: BioDocumentViewer: NCBI/EBI web services made easy
... BioDocumentViewer is a software to facilitate the use of public web services, [NCBI Entrez eUtils services][1] (NCBI, Bethesda, USA) and [EB-eye Search services][2] (EBI, Hinxton, UK). It provides you with a UI-based query builder, a document navigator, a batch sequence retrieval engine and sequen ...
ncbi ebi tool eutils ebe-eye written 24 months ago by patrick.durand120

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