Spectral Phasing Repository for "Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data" paper published at ECCB2016 and Bioinformatics Vol32 Issue 17.
Step 1. Compile and run SpectraPh.exe SAM2PSAM and follow instructions
Step 2. Run SpectraPh.exe PSAMBIN2CONTIGS and follow instructions
Step 3. Run Matlab ComputeCovariance.m
Step 4. Run Matlab ComputeEmbeddings.m
Step 5. Run Matlab ComputePhasing.m and see Results structure containing Phased HT-block ids per chromosome and their predicted haplotype id.
For additional help please be sure to read the github page, wiki and submit issues for any questions.
Animations are available at http://imgur.com/a/fwzBD
Relevant paper published at http://bioinformatics.oxfordjournals.org/content/32/17/i559.short