Jellyfish
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gmarcais
A fast multi-threaded k-mer counter
In jellyfish-2.3.0.tar.gz downloaded from the releases page, the LICENSE file says See the files LICENSE-BSD-3-Clause and LICENSE-GPL-3.0 for details. But these files are not included in the tarball. The probably...
I'm trying to find details on how exactly counts are stored in the *.jf file, but so far have been unable to find any. Any direction are welcome. Thanks
Hi, I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome...
Hello, I want to use jellyfish within my C code; I'm wondering if you have a C wrapper for your code? Thanks,
Hi! I am trying to calculate octomers in my libraries and I faced this weird problem ""Failed to open input file 'mer_counts.jf1021'. I am using version 2.2.6, it worked perfectly...
- Jelllyfish 2.3.0 - Clean install of Ubuntu 18.04 LTS - gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0 **Situation** When counting kmers and requesting a hash size that is larger than available memory,...
Hi @gmarcais Does Jellyfish support kmer counts per read or kmer count for an input (let's say echo ATCGACGTA | jellyfish [...] ? I saw your comment here stating that...
Hello I would like to count equally spaced k-mers. e.g.) in-frame k-mers (such as codons or bi-codons) with step size 3. Is it possible with Jellyfish? Thank you
Hi, I am trying to run jellyfish 1.1.12 for use with Quake. However, I noticed that my qdump files contain (many) zero counts. If I compare with the output of...
Hi Jellyfish group, I am trying to use jellyfish to generate kmer for a complete genome (~14G). I accidentally found some kmers should be in the genome but are not...
