LSA code has been cloned from https://github.com/brian-cleary/LatentStrainAnalysis. https://latentstrainanalysis.readthedocs.io/en/latest/getting_started.html
Python (2.7)
NumPy
SciPy
Gensim
GNU Parallel
Pyro4
spams
Hash and count k-mers :
bash HashCounting.sh 6 33 22
Cluster k-mers with NMF (100 clusters) :
bash KmerNMFClustering.sh 6 22 100
Partition reads :
bash ReadPartitioning.sh 4