gatb-core
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GATB
Core library of the Genome Analysis Toolbox with de-Bruijn graph
Hello, I wanted to read the beginner's doc but is unavailable due to respond time of gatb-core.gforge.inria.fr (yes I tried several browsers). Is there any way to circumvent this ?
Hello, How to use the Model Direct kmer type in the De Bruijn graph? apparently gatb-core seems to use only the ModelCanonical. Thanks, Lucas B. Rocha
Teo reports it freezes `RepartitorAlgorithm::execute()`
Hi! Is there any possibility to read a BAM file as a bank of sequences? Do you know of any software relying on GATB which would have done that? Thanks!
Hi, I am interested in using GATB in long reads analysis as they seem more appealing with HiFi reads and ultra-long ONT reads. Is GATB specifically for NGS short reads?...
Hello, I found https://github.com/GATB/gatb-core/commit/7cb8a48cc958f4266c74db57f02e937d583ba9b7 suggesting that this is synced with minia development, and indeed compiling minia with the latest release gives ``` /home/moeller/git/med-team/minia/minia/src/Minia.cpp:170:65: required from here /home/moeller/git/med-team/minia/minia/src/Minia.cpp:312:62: error: ‘class gatb::core::debruijn::impl::GraphUnitigsTemplate’...
Dear GATB team, In [pandora](https://github.com/rmcolq/pandora/), we use GATB to make a local assembly of de-novo variants. We are facing a performance issue where we have to perform several thousands local...
Hello all, I am using GATB library for my work. I have a naive question which I have not been able to find an answer for. While using one of...
There is a bug in the getDefaultProperties() function https://github.com/GATB/gatb-core/blob/e0c9525d53ab0a8da9d07512858c826a98a12da0/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp#L402 If we use an "OptionNoParam" to build an option that takes no parameters, it is always returned by getDefaultProperties(), I do...
Is there someone working on this ? The only reference I found is on the [GATB Global Architecture page](https://gatb.inria.fr/gatb-global-architecture/) : > Wrappers for other languages will be available in the...
