GitHub - srbehera11/KmerEstimate: KmerEstimate: A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage

Compile and Run

Compile:

	g++ -o kmerEst kmerCountEstimate.cpp -std=c++11 -O3 -march=native

Run:

	./KmerEst -f <seq.fa> -k  <kmerLen> -s <minHeap_Size> -c <coverage> -o <out.txt>

Name		Name	Last commit message	Last commit date
Latest commit History 43 Commits
sparsepp		sparsepp
LICENSE		LICENSE
MurmurHash3.c		MurmurHash3.c
MurmurHash3.h		MurmurHash3.h
README.md		README.md
kmerCountEstimate		kmerCountEstimate
kmerCountEstimate.cpp		kmerCountEstimate.cpp
kmerEst		kmerEst
kmerEst.err		kmerEst.err
kmerEst.out		kmerEst.out
kseq.h		kseq.h
metrohash64.cpp		metrohash64.cpp
metrohash64.h		metrohash64.h
ntHashIterator.hpp		ntHashIterator.hpp
nthash.hpp		nthash.hpp
platform.h		platform.h
runKmerEst.slurm		runKmerEst.slurm