KmerInShort counts kmers from a fasta/fastq file or list of files, and outputs results in a text file. It is limited to short kmers (k<15). It is a part of the FEELnc pipeline from V.Wucher, F.Legai and T.Derrien, a pipeline to annotate long non-coding RNAs.
To retrieve KmerInShort and its submodule (gatb-core), type
git clone --recursive https://github.com/rizkg/KmerInShort
Then build the tool with
mkdir build; cd build; cmake ..; make -j 8
KmerinShort is also able to compute the Normalized shannon entropy (NSE) of a dataset, as defined by F.Onate et al (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373121/)
./KmerInShort -file file.fastq.gz -kmer-size 4 -nb-cores 8 -out result4s -sum -NSE
Guillaume Rizk [email protected]