GitHub - jamshed/KmerEstimate_Project: A project submitted as the requirement of the course CSE 549 (Computational Biology), titled as "Efficient Parallelization for KmerEstimate: A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage". Original serial algorithm available at github.com/srbehera11/KmerEstimate.

Compile and Run

Compile original algorithm implementation:

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

Compile parallel algorithm implementation(s):

	g++ -o monitor Monitor.cpp -std=c++11 -O3 -march=native -pthread
	
	g++ -o spinlock Spinlock.cpp -std=c++11 -O3 -march=native -pthread

Run original (serial) algorithm implementation:

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

Run parallel (multi-threaded) algorithm implementation (Monitor i.e. lock and conditional-variable based approach):

	./monitor -f <seq.fa> -k  <kmerLen> -s <minHeap_Size> -t <thread count> -c <coverage> -o <out.txt>

Run parallel (multi-threaded) algorithm implementation (Spinlock based approach):

	./spinlock -f <seq.fa> -k  <kmerLen> -s <minHeap_Size> -t <thread count> -c <coverage> -o <out.txt>

Name		Name	Last commit message	Last commit date
Latest commit History 30 Commits
MoreOutputs		MoreOutputs
Outputs		Outputs
Test Codes		Test Codes
sparsepp		sparsepp
.gitignore		.gitignore
LICENSE		LICENSE
Monitor.cpp		Monitor.cpp
README.md		README.md
Spinlock.cpp		Spinlock.cpp
kmerCountEstimate.cpp		kmerCountEstimate.cpp
kmerEst		kmerEst
kseq.h		kseq.h
metrohash64.cpp		metrohash64.cpp
metrohash64.h		metrohash64.h
monitor		monitor
ntHashIterator.hpp		ntHashIterator.hpp
nthash.hpp		nthash.hpp
platform.h		platform.h
spinlock		spinlock