User: edrezen

gravatar for edrezen
edrezen700
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700
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France
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15 hours ago
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4 years, 2 months ago
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e******@irisa.fr

Posts by edrezen

<prev • 76 results • page 1 of 8 • next >
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Comment: C: Fast Interval Intersection Methodologies
... I would suggest usage of [pybind11][1] to write such a python extension; this amazing library is really a good choice to expose fast C++ algorithms implementations in python in order to make them more popular as Istvan said. [1]: https://github.com/pybind/pybind11 ...
written 8 months ago by edrezen700
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Comment: C: Bug in JellyFish and DSK k-mer counting tool?
... DSK indeed will use a canonical form of the kmer that corresponds to the minimum value of the kmer and its reverse-complement. So in the example one should grep ACTTGCAGCCGCCACAATGGGTGTTATGTAA. ...
written 19 months ago by edrezen700
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Answer: A: Getting list of connected nodes to a node
... Hello, You could have a look [here][1], in particular the "successor" method of the Graph class. [1]: http://gatb-core.gforge.inria.fr/doc/api/snippets_graph.html#snippets_dbg_3 ...
written 21 months ago by edrezen700
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Comment: C: running SOAP using 32G RAM
... You can have a look [here][1] about Minia, in particular Table 2 to have an idea of memory usage of Minia. [1]: http://minia.genouest.org/ ...
written 22 months ago by edrezen700
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Comment: C: LoRDEC correction insufficient memory error
... The issue occurs during the kmer counting algorithm of the GATB library; I think this bug has been corrected in the latest version of the library 1.2.0. **However**, there are some API changes in the GATB library 1.2.0 so it is not usable as it with lordec. The best shot you have right now is to p ...
written 2.2 years ago by edrezen700
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Comment: C: Minia crashes during kmer counting
... You have a point here: for kmer size >= 128, the default algorithm of one part of the de Bruijn algorithm (cascading BLoom filters) can't work. In such a case, a specific option has to be used, ie. you should add **-debloom original** in your minia command line (the consequence is a bigger memo ...
written 2.2 years ago by edrezen700
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Comment: C: hash function for DNA sequences
... Take for instance the kmer K=GTCGAATC (size 8) If you take by convention A=0, C=1, G=2, T=3, you can encode K as a polynomial in base 4 like this: K = G.4^0 + T.4^1 + C.4^2 + G.4^3 + A.4^4 + A.4^5 + T.4^6 + C.4^7 K = 2*4^0 + 3*4^1 + 1*4^2 + 2*4^3 + 0*4^4 + 0*4^5 + 3*4^6 + 1*4^7 K = 28 ...
written 2.3 years ago by edrezen700
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Answer: A: problem compiling discoSnp++ make: *** No targets specified and no makefile fo
... Hello, DiscoSNP++ requires that the [cmake][1] tool is installed on your machine (see the trace "cmake: command not found") You have to install cmake first before building DiscoSNP++. [1]: https://cmake.org/ ...
written 2.3 years ago by edrezen700
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Comment: C: C++ tools are hard to install for biologist, why the community stick on it?
... I strongly agree with Rob's comment about the great control over memory coming with c++. Moreover, I am not sure at 100% that java takes advantage to use specific hardware features as SSE registers for instance (which allows to vectorize some algorithms with great speedups) Note that I am a great ...
written 2.4 years ago by edrezen700
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Comment: C: Internal memory allocator is full!
... Hello, I think you are using an old version of minia. You should have a try to the new one here (much faster with improved result quality); there are chances that you won't face the same memory issues with this new version. ...
written 2.4 years ago by edrezen700

Latest awards to edrezen

Popular Question 3 months ago, created a question with more than 1,000 views. For New version of the GATB library
Popular Question 4 months ago, created a question with more than 1,000 views. For Life cycle of a fastq file
Popular Question 7 months ago, created a question with more than 1,000 views. For All-in-one NCBI / EBI / Amazon BLAST workstation
Popular Question 2.2 years ago, created a question with more than 1,000 views. For KLAST, a Blast-like tool for fast sequence similarity searches: free academic version
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: hash function for DNA sequences
Scholar 3.0 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 3.2 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 3.3 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Supporter 3.3 years ago, voted at least 25 times.
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Scholar 4.0 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models

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