ParallelKmerEstimate

A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage in Parallel.

Usage

g++ -o pkmerEst parallelKmerCountEstimate.cpp -std=c++11 -O3 -march=native

./pkmerEst -f <seq.fa> -k  <kmerLen> -s <minHeap_Size> -c <coverage> -t <thread_count> -q <queue_size> -o <out.txt>

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
sparsepp		sparsepp
LICENSE		LICENSE
MurmurHash3.c		MurmurHash3.c
MurmurHash3.h		MurmurHash3.h
ParallelKmerEstimate.pdf		ParallelKmerEstimate.pdf
README.md		README.md
kmerCountEstimate.cpp		kmerCountEstimate.cpp
kmerEst.out		kmerEst.out
kseq.h		kseq.h
metrohash64.cpp		metrohash64.cpp
metrohash64.h		metrohash64.h
ntHashIterator.hpp		ntHashIterator.hpp
nthash.hpp		nthash.hpp
output.txt		output.txt
parallelKmerCountEstimate.cpp		parallelKmerCountEstimate.cpp
pkmerEst		pkmerEst
platform.h		platform.h
runKmerEst.slurm		runKmerEst.slurm