Awesome

KmerInShort

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.

Installation

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

example usage for NSE calculation

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

Author

Guillaume Rizk guillaume.rizk@algorizk.com