This fork for WhatsHap explores the application of the minimum error correction approach to sequences embedded in graphs. Its goal is to enable the phasing of complex loci that arise during genome assembly, which cannot be assembled by alignment, and which instead require phasing and haplotype inference to resolve.
To partition a path set in a graph, simply provide a sorted GFA file to whatshap_graph.py:
python whatshap_graph.py graph.gfa >graph.partition.tsv
The results can be used to subset the sequences embedded in the graph for reassembly.
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
For documentation and information on how to cite WhatsHap, please visit the WhatsHap Homepage