Jellyfish
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gmarcais
A fast multi-threaded k-mer counter
Hello, I am trying to use [HAWK](https://github.com/atifrahman/HAWK) to count kmers in Illumina reads. HAWK used a modified version of jellyfish 1.1.6, though the extent to which it is modified is...
Hi - I am trying to run jellyfish 2.2.10 as part of the Trinity 2.8.4 pipeline. I have the following error: ``` Jellyfish/2.2.10/bin/.libs/lt-jellyfish: symbol lookup error: Jellyfish/2.2.10/bin/.libs/lt-jellyfish: undefined symbol: _ZNK9jellyfish23RectangularBinaryMatrix15is_low_identityEv...
Hi, I have created a db (canoncical) with 51mers. When i run query sequence of 51bp (25bp-SNP-25bp) it'll mostly return counts of 0. However if i lengthen those query sequences...
Follow the binding tutorail in the jellyfish page to build with python bindings, but when I try to import jellyfish got the following error ``` >>> import jellyfish Traceback (most...
fails on ubuntu 16.04 LTS. Log is attached below. See #119 [2.2.10.makefail.txt](https://github.com/gmarcais/Jellyfish/files/1996094/2.2.10.makefail.txt)
I'm surprised that this feature isn't in the issues or documentation (that I see), but I'd like to create a kmer count table for multiple metagenome samples (kmer x sample...
Hi Guillaume, Super happy to find Jellyfish and it really helps for my kmer job. I have a question about the histo subcommand. I want to count the numbers of...
hello, I wonder if it is possible estimate the heterozygosity present in my sequencing reads from a distribution like this:  It is from raw Illumina reads of a heterozygous...
If the read name containing each can be found, I think jellyfish can be used to do more creative work, rather than just counting kmer, e.g. remove reads with some...
Hi all, I try to install jellyfish on my cluster. When I try 2.2.7 I get the following: Output of: `./configure --prefix=/home/usr9/z41809w/jellytest` ``` checking build system type... x86_64-pc-linux-gnu checking host...
