Haplotype threading

Here are the scripts for pan-genome graph based haplotype threading with short reads (by Craig Dent)

ANALYSIS.sh gives the pipeline, where the example data can be downloaded here: https://mega.nz/folder/S8shkDhD#aJKNU8QAnUWi3qWUNcKGpA

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
ANALYSIS.sh		ANALYSIS.sh
LICENSE		LICENSE
README.md		README.md
a0_convert_dumpsFasta_to_tsv.py		a0_convert_dumpsFasta_to_tsv.py
a0_convert_nodekmers_to_fasta.sh		a0_convert_nodekmers_to_fasta.sh
a1_fitPeaks_v7.py		a1_fitPeaks_v7.py
a2_EM.v0.4.py		a2_EM.v0.4.py
a2_get_kmer_stats.py		a2_get_kmer_stats.py
a2_sort_and_fill_nodekstats.py		a2_sort_and_fill_nodekstats.py
a3_threading_getStats_WhiteRose_v7.py		a3_threading_getStats_WhiteRose_v7.py
a3_threading_simpleImputeV7_WhiteRose.py		a3_threading_simpleImputeV7_WhiteRose.py

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