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1. VCF-Simplify VCF-Simplify Public

   A python parser to simplify and build the VCF (Variant Call Format).

   Python 45 11

2. phase-extender phase-extender Public

   A python program that uses ReadBack phased haplotypes in population of samples and returns extended haplotype blocks.

   Jupyter Notebook 13 4

3. phase-stitcher phase-stitcher Public

   a python program to stitch the ReadBack phased haplotypes in F1 hybrids.

   Jupyter Notebook 6 3

4. ASE-CADG ASE-CADG Public

   Pipeline for ASE (allele specific expression) using competitive alignment to diploid genome

   HTML 3

5. SmallTools SmallTools Public

   Collection of several small tools. These tools stay here temporarily and may move to other major repositories as they evolve.

   Python 2

6. TestSwitchErrors TestSwitchErrors Public

   This is a tutorial that shows how phaseExtender can be used for recursive improvement of haplotype phasing and how to test the phasing quality by measuring switcherrors.

   Jupyter Notebook 2