Jellyfish
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gmarcais
A fast multi-threaded k-mer counter
Greetings, with the recent introduction of Gcc 12 in Debian _experimental_, Matthias Klose noticed in [Debian Bug#1012953](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012953) that Jellyfish fails to build from source using _g++-12_. Relevant part of the...
I can count on one hand bioinformatics programs I actually like, and with these new arbitrary kmer sizes, swig, and bloom filters, Jellyfish is about to make it there. Really...
I am experiencing the following issue with the `query` command. I've build a kmer database from hg38 using the following command: `jellyfish count -m 15 -t 5 -s 100M -L...
Can Jellyfish read gzipped fastq files and, if not, can uncompressed fastq be piped into Jellyfish. Thanks,
Hi, I'm trying to figure out how I twist around the source code to let the software handle ambiguous characters (N, for example). Any help would be greatly appreciated!
Hi, I'd like to use just the multithreaded hashmap implementation from jellyfish in a C++ application, as well as the key encoding, if that's separate. Is this available anywhere? One...
I think the `libool` dependency (for compiling from the git tree) is `libtool`?
Hi @gmarcais, I'm adding Jellyfish to Nix repo so that it can be installed via `nixpkgs` as well. Could I add you to its maintainers as well? https://github.com/NixOS/nixpkgs/pull/143066
I ran "jellyfish count" command on PacBio Hifi reads in fasta format to get the k-mer count statistics. But the execution fails with "Error: can't open file output.jellyfish1021" which is...
